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HEADER OXYGEN TRANSPORT 23-AUG-96 1BIN TITLE LEGHEMOGLOBIN A (ACETOMET) COMPND MOL_ID: 1; COMPND 2 MOLECULE: LEGHEMOGLOBIN A; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: ACETOMET SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GLYCINE MAX; SOURCE 3 ORGANISM_COMMON: SOYBEAN; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI KEYWDS HEME, NITROGEN FIXATION, MULTIGENE FAMILY, OXYGEN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR E.A.BRUCKER,M.S.HARGROVE,G.N.PHILLIPS JR. REVDAT 3 03-MAY-05 1BIN 1 AUTHOR JRNL REVDAT 2 01-APR-03 1BIN 1 JRNL REVDAT 1 12-MAR-97 1BIN 0 JRNL AUTH M.S.HARGROVE,J.K.BARRY,E.A.BRUCKER,M.B.BERRY, JRNL AUTH 2 G.N.PHILLIPS JR.,J.S.OLSON,R.ARREDONDO-PETER, JRNL AUTH 3 J.M.DEAN,R.V.KLUCAS,G.SARATH JRNL TITL CHARACTERIZATION OF RECOMBINANT SOYBEAN JRNL TITL 2 LEGHEMOGLOBIN A AND APOLAR DISTAL HISTIDINE JRNL TITL 3 MUTANTS. JRNL REF J.MOL.BIOL. V. 266 1032 1997 JRNL REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 85.7 REMARK 3 NUMBER OF REFLECTIONS : 12099 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.297 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 : 2626 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 102 REMARK 3 SOLVENT ATOMS : 410 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) : 0.018 REMARK 3 BOND ANGLES (DEGREES) : 1.93 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 2.29 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 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 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : PARAMETER.HEME REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TOPOLOGY.HEME REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1BIN 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 (2007-03-16) REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 295.0 REMARK 200 PH : 6.80 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 : SIEMENS 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 AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : R-AXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26287 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 85.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.10300 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: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.8 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 17.49000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 70.86500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.69500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 70.86500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.49000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.69500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 350 BIOMOLECULE: 2 REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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: 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 ILE A 22 CG1 ILE A 22 CD1 0.133 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 VAL A 97 N - CA - C ANGL. DEV. =-13.8 DEGREES REMARK 500 THR A 98 N - CA - C ANGL. DEV. =-14.9 DEGREES REMARK 500 ILE B 22 CG1 - CB - CG2 ANGL. DEV. =-13.0 DEGREES REMARK 500 LYS B 95 N - CA - C ANGL. DEV. = 17.8 DEGREES REMARK 500 VAL B 97 N - CA - C ANGL. DEV. =-12.9 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 266 DISTANCE = 5.56 ANGSTROMS DBREF 1BIN A 1 143 UNP P02238 LGBA_SOYBN 1 143 DBREF 1BIN B 1 143 UNP P02238 LGBA_SOYBN 1 143 SEQRES 1 A 143 VAL ALA PHE THR GLU LYS GLN ASP ALA LEU VAL SER SER SEQRES 2 A 143 SER PHE GLU ALA PHE LYS ALA ASN ILE PRO GLN TYR SER SEQRES 3 A 143 VAL VAL PHE TYR THR SER ILE LEU GLU LYS ALA PRO ALA SEQRES 4 A 143 ALA LYS ASP LEU PHE SER PHE LEU ALA ASN GLY VAL ASP SEQRES 5 A 143 PRO THR ASN PRO LYS LEU THR GLY HIS ALA GLU LYS LEU SEQRES 6 A 143 PHE ALA LEU VAL ARG ASP SER ALA GLY GLN LEU LYS ALA SEQRES 7 A 143 SER GLY THR VAL VAL ALA ASP ALA ALA LEU GLY SER VAL SEQRES 8 A 143 HIS ALA GLN LYS ALA VAL THR ASP PRO GLN PHE VAL VAL SEQRES 9 A 143 VAL LYS GLU ALA LEU LEU LYS THR ILE LYS ALA ALA VAL SEQRES 10 A 143 GLY ASP LYS TRP SER ASP GLU LEU SER ARG ALA TRP GLU SEQRES 11 A 143 VAL ALA TYR ASP GLU LEU ALA ALA ALA ILE LYS LYS ALA SEQRES 1 B 143 VAL ALA PHE THR GLU LYS GLN ASP ALA LEU VAL SER SER SEQRES 2 B 143 SER PHE GLU ALA PHE LYS ALA ASN ILE PRO GLN TYR SER SEQRES 3 B 143 VAL VAL PHE TYR THR SER ILE LEU GLU LYS ALA PRO ALA SEQRES 4 B 143 ALA LYS ASP LEU PHE SER PHE LEU ALA ASN GLY VAL ASP SEQRES 5 B 143 PRO THR ASN PRO LYS LEU THR GLY HIS ALA GLU LYS LEU SEQRES 6 B 143 PHE ALA LEU VAL ARG ASP SER ALA GLY GLN LEU LYS ALA SEQRES 7 B 143 SER GLY THR VAL VAL ALA ASP ALA ALA LEU GLY SER VAL SEQRES 8 B 143 HIS ALA GLN LYS ALA VAL THR ASP PRO GLN PHE VAL VAL SEQRES 9 B 143 VAL LYS GLU ALA LEU LEU LYS THR ILE LYS ALA ALA VAL SEQRES 10 B 143 GLY ASP LYS TRP SER ASP GLU LEU SER ARG ALA TRP GLU SEQRES 11 B 143 VAL ALA TYR ASP GLU LEU ALA ALA ALA ILE LYS LYS ALA HET ACT A 145 4 HET ACT B 145 4 HET SO4 200 5 HET HEM A 144 43 HET HEM B 144 43 HETNAM ACT ACETATE ION HETNAM SO4 SULFATE ION HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 3 ACT 2(C2 H3 O2 1-) FORMUL 5 SO4 O4 S 2- FORMUL 6 HEM 2(C34 H32 FE N4 O4) FORMUL 8 HOH *135(H2 O) HELIX 1 AA GLU A 5 PHE A 18 1 14 HELIX 2 AB ILE A 22 LYS A 36 1 15 HELIX 3 AC PRO A 38 ASP A 42 1 5 HELIX 4 AD SER A 45 LEU A 47 1 3 HELIX 5 AE PRO A 56 SER A 79 1 24 HELIX 6 AF ALA A 86 ALA A 93 1 8 HELIX 7 AG ASP A 99 VAL A 117 1 19 HELIX 8 AH ASP A 123 LYS A 141 1 19 HELIX 9 BA GLU B 5 PHE B 18 1 14 HELIX 10 BB ILE B 22 LYS B 36 1 15 HELIX 11 BC PRO B 38 ASP B 42 1 5 HELIX 12 BD SER B 45 LEU B 47 1 3 HELIX 13 BE PRO B 56 SER B 79 1 24 HELIX 14 BF ALA B 86 ALA B 93 1 8 HELIX 15 BG ASP B 99 VAL B 117 1 19 HELIX 16 BH ASP B 123 LYS B 141 1 19 LINK FE HEM A 144 NE2 HIS A 92 LINK FE HEM A 144 O ACT A 145 LINK FE HEM B 144 NE2 HIS B 92 LINK FE HEM B 144 O ACT B 145 CRYST1 34.980 53.390 141.730 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 0.028588 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018730 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007056 0.00000