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HEADER OXIDOREDUCTASE 24-APR-00 1EW6 TITLE THE CRYSTAL STRUCTURE AND AMINO ACID SEQUENCE OF TITLE 2 DEHALOPEROXIDASE FROM AMPHITRITE ORNATA INDICATE COMMON TITLE 3 ANCESTRY WITH GLOBINS COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEHALOPEROXIDASE; COMPND 3 CHAIN: A, B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AMPHITRITE ORNATA; SOURCE 3 ORGANISM_COMMON: MARINE WORM; SOURCE 4 OTHER_DETAILS: POLYCHAETE KEYWDS GLOBIN, HALOPHENOLS EXPDTA X-RAY DIFFRACTION AUTHOR L.LEBIODA REVDAT 3 01-APR-03 1EW6 1 JRNL REVDAT 2 06-SEP-00 1EW6 1 JRNL REVDAT 1 10-MAY-00 1EW6 0 JRNL AUTH M.W.LACOUNT,E.ZHANG,Y.P.CHEN,K.HAN,M.M.WHITTON, JRNL AUTH 2 D.E.LINCOLN,S.A.WOODIN,L.LEBIODA JRNL TITL THE CRYSTAL STRUCTURE AND AMINO ACID SEQUENCE OF JRNL TITL 2 DEHALOPEROXIDASE FROM AMPHITRITE ORNATA INDICATE JRNL TITL 3 COMMON ANCESTRY WITH GLOBINS. JRNL REF J.BIOL.CHEM. V. 275 18712 2000 JRNL REFN ASTM JBCHA3 US ISSN 0021-9258 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.78 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.78 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 24637 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 2000 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2192 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 96 REMARK 3 SOLVENT ATOMS : 107 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.30 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1EW6 COMPLIES WITH FORMAT V. 3.0, 1-DEC-2006 REMARK 4 REMARK 4 THIS IS THE REMEDIATED VERSION OF THIS PDB ENTRY. REMARK 4 REMEDIATED DATA FILE REVISION 3.100 (2007-03-17) REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB . REMARK 100 THE RCSB ID CODE IS RCSB010951. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-OCT-1995 REMARK 200 TEMPERATURE (KELVIN) : 298.0 REMARK 200 PH : 7.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS II REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24637 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.780 REMARK 200 RESOLUTION RANGE LOW (A) : 10.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 2.300 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, 200 MM AMMONIUM SULFATE, REMARK 280 PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 1/2-X,-Y,1/2+Z REMARK 290 3555 -X,1/2+Y,1/2-Z REMARK 290 4555 1/2+X,1/2-Y,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 34.25000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.50000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.20000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.50000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.25000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.20000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI REMARK 500 O HOH 105 O HOH 107 2.06 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),F6.3) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 PHE A 35 N PHE A 35 CA -0.064 REMARK 500 PHE A 35 CB PHE A 35 CG 0.076 REMARK 500 PHE A 35 CA PHE A 35 C 0.066 REMARK 500 TYR A 34 C PHE A 35 N -0.057 REMARK 500 SER A 90 CA SER A 90 C 0.068 REMARK 500 SER A 91 CA SER A 91 CB -0.099 REMARK 500 SER A 91 CA SER A 91 C 0.053 REMARK 500 SER A 90 C SER A 91 N -0.137 REMARK 500 SER A 91 C LEU A 92 N -0.059 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PHE A 35 CA - CB - CG ANGL. DEV. = 8.4 DEGREES REMARK 500 MET A 86 N - CA - C ANGL. DEV. = -7.4 DEGREES REMARK 500 SER A 91 N - CA - CB ANGL. DEV. =-19.3 DEGREES REMARK 500 SER A 91 CA - CB - OG ANGL. DEV. = -7.1 DEGREES REMARK 500 SER A 91 C - N - CA ANGL. DEV. = 9.5 DEGREES REMARK 500 LEU A 92 N - CA - C ANGL. DEV. = 7.8 DEGREES REMARK 500 LEU B 13 N - CA - C ANGL. DEV. = 7.5 DEGREES REMARK 500 ASN B 37 N - CA - C ANGL. DEV. = 7.6 DEGREES REMARK 500 HIS B 55 CA - CB - CG ANGL. DEV. = 11.6 DEGREES REMARK 525 REMARK 525 SOLVENT REMARK 525 THE FOLLOWING SOLVENT MOLECULES LIE FARTHER THAN EXPECTED REMARK 525 FROM THE PROTEIN OR NUCLEIC ACID MOLECULE AND MAY BE REMARK 525 ASSOCIATED WITH A SYMMETRY RELATED MOLECULE (M=MODEL REMARK 525 NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH 7 DISTANCE = 5.17 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1EWA RELATED DB: PDB DBREF 1EW6 A 1 137 UNP Q9NAV8 Q9NAV8_9ANNE 2 138 DBREF 1EW6 B 1 137 UNP Q9NAV8 Q9NAV8_9ANNE 2 138 SEQRES 1 A 137 GLY PHE LYS GLN ASP ILE ALA THR ILE ARG GLY ASP LEU SEQRES 2 A 137 ARG THR TYR ALA GLN ASP ILE PHE LEU ALA PHE LEU ASN SEQRES 3 A 137 LYS TYR PRO ASP GLU ARG ARG TYR PHE LYS ASN TYR VAL SEQRES 4 A 137 GLY LYS SER ASP GLN GLU LEU LYS SER MET ALA LYS PHE SEQRES 5 A 137 GLY ASP HIS THR GLU LYS VAL PHE ASN LEU MET MET GLU SEQRES 6 A 137 VAL ALA ASP ARG ALA THR ASP CYS VAL PRO LEU ALA SER SEQRES 7 A 137 ASP ALA ASN THR LEU VAL GLN MET LYS GLN HIS SER SER SEQRES 8 A 137 LEU THR THR GLY ASN PHE GLU LYS LEU PHE VAL ALA LEU SEQRES 9 A 137 VAL GLU TYR MET ARG ALA SER GLY GLN SER PHE ASP SER SEQRES 10 A 137 GLN SER TRP ASP ARG PHE GLY LYS ASN LEU VAL SER ALA SEQRES 11 A 137 LEU SER SER ALA GLY MET LYS SEQRES 1 B 137 GLY PHE LYS GLN ASP ILE ALA THR ILE ARG GLY ASP LEU SEQRES 2 B 137 ARG THR TYR ALA GLN ASP ILE PHE LEU ALA PHE LEU ASN SEQRES 3 B 137 LYS TYR PRO ASP GLU ARG ARG TYR PHE LYS ASN TYR VAL SEQRES 4 B 137 GLY LYS SER ASP GLN GLU LEU LYS SER MET ALA LYS PHE SEQRES 5 B 137 GLY ASP HIS THR GLU LYS VAL PHE ASN LEU MET MET GLU SEQRES 6 B 137 VAL ALA ASP ARG ALA THR ASP CYS VAL PRO LEU ALA SER SEQRES 7 B 137 ASP ALA ASN THR LEU VAL GLN MET LYS GLN HIS SER SER SEQRES 8 B 137 LEU THR THR GLY ASN PHE GLU LYS LEU PHE VAL ALA LEU SEQRES 9 B 137 VAL GLU TYR MET ARG ALA SER GLY GLN SER PHE ASP SER SEQRES 10 B 137 GLN SER TRP ASP ARG PHE GLY LYS ASN LEU VAL SER ALA SEQRES 11 B 137 LEU SER SER ALA GLY MET LYS HET SO4 150 5 HET SO4 151 5 HET HEM A 139 43 HET HEM B 139 43 HETNAM SO4 SULFATE ION HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 HEM 2(C34 H32 FE N4 O4) FORMUL 7 HOH *107(H2 O) HELIX 1 1 GLY A 1 ASP A 12 1 12 HELIX 2 2 ASP A 12 TYR A 28 1 17 HELIX 3 3 PRO A 29 PHE A 35 5 7 HELIX 4 4 PHE A 35 VAL A 39 5 5 HELIX 5 5 SER A 42 MET A 49 1 8 HELIX 6 6 MET A 49 ALA A 70 1 22 HELIX 7 7 LEU A 76 GLN A 85 1 10 HELIX 8 8 MET A 86 SER A 90 5 5 HELIX 9 9 THR A 93 SER A 111 1 19 HELIX 10 10 ASP A 116 ALA A 134 1 19 HELIX 11 11 GLY B 1 ASP B 12 1 12 HELIX 12 12 ASP B 12 TYR B 28 1 17 HELIX 13 13 PRO B 29 PHE B 35 5 7 HELIX 14 14 PHE B 35 VAL B 39 5 5 HELIX 15 15 SER B 42 SER B 48 1 7 HELIX 16 16 MET B 49 ALA B 70 1 22 HELIX 17 17 LEU B 76 MET B 86 1 11 HELIX 18 18 LYS B 87 SER B 90 5 4 HELIX 19 19 THR B 93 SER B 111 1 19 HELIX 20 20 ASP B 116 ALA B 134 1 19 LINK NE2 HIS A 89 FE HEM A 139 LINK NE2 HIS B 89 FE HEM B 139 CRYST1 68.500 68.400 61.000 90.00 90.00 90.00 P 21 21 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.014599 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014620 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016393 0.00000