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HEADER OXYGEN STORAGE/TRANSPORT 22-JAN-04 1S5X TITLE THE CRYSTAL STRUCTURE OF TREMATOMUS BERNACCHII HEMOGLOBIN TITLE 2 OXIDIZED BY AIR COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEMOGLOBIN ALPHA CHAIN; COMPND 3 CHAIN: A; COMPND 4 MOL_ID: 2; COMPND 5 MOLECULE: HEMOGLOBIN BETA CHAIN; COMPND 6 CHAIN: B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PAGOTHENIA BERNACCHII; SOURCE 3 ORGANISM_COMMON: EMERALD ROCKCOD; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: PAGOTHENIA BERNACCHII; SOURCE 6 ORGANISM_COMMON: EMERALD ROCKCOD KEYWDS HEMICHROME, BIS-HISTIDINE, OXIDATION EXPDTA X-RAY DIFFRACTION AUTHOR L.VITAGLIANO,G.BONOMI,A.RICCIO,G.DI PRISCO,G.SMULEVICH, AUTHOR 2 L.MAZZARELLA REVDAT 1 04-MAY-04 1S5X 0 JRNL AUTH L.VITAGLIANO,G.BONOMI,A.RICCIO,G.DI PRISCO, JRNL AUTH 2 G.SMULEVICH,L.MAZZARELLA JRNL TITL THE OXIDATION PROCESS OF ANTARCTIC FISH HEMOGLOBINS JRNL REF EUR.J.BIOCHEM. V. 271 1651 2004 JRNL REFN ASTM EJBCAI IX ISSN 0014-2956 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.RICCIO,L.VITAGLIANO,G.DI PRISCO,A.ZAGARI, REMARK 1 AUTH 2 L.MAZZARELLA REMARK 1 TITL THE CRYSTAL STRUCTURE OF A TETRAMERIC HEMOGLOBIN REMARK 1 TITL 2 IN A PARTIAL HEMICHROME STATE REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 99 9801 2002 REMARK 1 REFN ASTM PNASA6 US ISSN 0027-8424 REMARK 2 REMARK 2 RESOLUTION. 2.40 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 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) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 12438 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) : 0.190 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1087 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 : 2154 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 86 REMARK 3 SOLVENT ATOMS : 27 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) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 1.40 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 17.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.93 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 1S5X 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 3.101 (2007-05-29) REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ. REMARK 100 THE RCSB ID CODE IS RCSB021407. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JUL-2002 REMARK 200 TEMPERATURE (KELVIN) : 293.0 REMARK 200 PH : 7.60 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 : ENRAF-NONIUS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : DIP 2030B REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XPRESS, DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14020 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.34600 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPEG 5000, TRIS, PH 7.6, LIQUID REMARK 280 DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 1/2+X,1/2+Y,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 54.25800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.54750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 54.25800 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 32.54750 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 PHE B 45 REMARK 465 GLY B 46 REMARK 465 ASN B 47 REMARK 465 LEU B 48 REMARK 465 TYR B 49 REMARK 465 ASN B 50 REMARK 465 ALA B 51 REMARK 465 GLU B 52 REMARK 465 TYR B 145 REMARK 465 HIS B 146 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 MET A 82 SD MET A 82 CE 0.058 REMARK 500 MET A 113 SD MET A 113 CE 0.054 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 SER A 1 O - C - N ANGL. DEV. =-19.1 DEGREES REMARK 500 LEU A 2 C - N - CA ANGL. DEV. = 9.6 DEGREES REMARK 500 TYR A 90 N - CA - C ANGL. DEV. = 8.6 DEGREES REMARK 500 THR B 4 N - CA - C ANGL. DEV. = -8.9 DEGREES REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1LA6 RELATED DB: PDB REMARK 900 RELATED ID: 1S5Y RELATED DB: PDB REMARK 900 THE SAME PROTEIN OXIDIZED BY FERRICYANIDE DBREF 1S5X A 1 142 UNP P80043 HBA_PAGBE 1 142 DBREF 1S5X B 1 146 UNP P80044 HBB_PAGBE 1 146 SEQRES 1 A 142 SER LEU SER ASP LYS ASP LYS ALA ALA VAL ARG ALA LEU SEQRES 2 A 142 TRP SER LYS ILE GLY LYS SER ALA ASP ALA ILE GLY ASN SEQRES 3 A 142 ASP ALA LEU SER ARG MET ILE VAL VAL TYR PRO GLN THR SEQRES 4 A 142 LYS THR TYR PHE SER HIS TRP PRO ASP VAL THR PRO GLY SEQRES 5 A 142 SER PRO HIS ILE LYS ALA HIS GLY LYS LYS VAL MET GLY SEQRES 6 A 142 GLY ILE ALA LEU ALA VAL SER LYS ILE ASP ASP LEU LYS SEQRES 7 A 142 THR GLY LEU MET GLU LEU SER GLU GLN HIS ALA TYR LYS SEQRES 8 A 142 LEU ARG VAL ASP PRO ALA ASN PHE LYS ILE LEU ASN HIS SEQRES 9 A 142 CYS ILE LEU VAL VAL ILE SER THR MET PHE PRO LYS GLU SEQRES 10 A 142 PHE THR PRO GLU ALA HIS VAL SER LEU ASP LYS PHE LEU SEQRES 11 A 142 SER GLY VAL ALA LEU ALA LEU ALA GLU ARG TYR ARG SEQRES 1 B 146 VAL GLU TRP THR ASP LYS GLU ARG SER ILE ILE SER ASP SEQRES 2 B 146 ILE PHE SER HIS MET ASP TYR ASP ASP ILE GLY PRO LYS SEQRES 3 B 146 ALA LEU SER ARG CYS LEU ILE VAL TYR PRO TRP THR GLN SEQRES 4 B 146 ARG HIS PHE SER GLY PHE GLY ASN LEU TYR ASN ALA GLU SEQRES 5 B 146 ALA ILE ILE GLY ASN ALA ASN VAL ALA ALA HIS GLY ILE SEQRES 6 B 146 LYS VAL LEU HIS GLY LEU ASP ARG GLY VAL LYS ASN MET SEQRES 7 B 146 ASP ASN ILE ALA ALA THR TYR ALA ASP LEU SER THR LEU SEQRES 8 B 146 HIS SER GLU LYS LEU HIS VAL ASP PRO ASP ASN PHE LYS SEQRES 9 B 146 LEU LEU SER ASP CYS ILE THR ILE VAL LEU ALA ALA LYS SEQRES 10 B 146 MET GLY HIS ALA PHE THR ALA GLU THR GLN GLY ALA PHE SEQRES 11 B 146 GLN LYS PHE LEU ALA VAL VAL VAL SER ALA LEU GLY LYS SEQRES 12 B 146 GLN TYR HIS HET ACE A 0 3 HET HEM A 200 43 HET HEM B 400 43 HETNAM ACE ACETYL GROUP HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 3 ACE C2 H4 O FORMUL 4 HEM 2(C34 H32 FE N4 O4) FORMUL 6 HOH *27(H2 O) HELIX 1 1 SER A 3 GLY A 18 1 16 HELIX 2 2 SER A 20 TYR A 36 1 17 HELIX 3 3 PRO A 37 SER A 44 5 8 HELIX 4 4 SER A 53 LYS A 73 1 21 HELIX 5 5 ASP A 76 LEU A 81 1 6 HELIX 6 6 LEU A 81 LYS A 91 1 11 HELIX 7 7 ALA A 97 PHE A 114 1 18 HELIX 8 8 THR A 119 GLU A 139 1 21 HELIX 9 9 ARG A 140 ARG A 142 5 3 HELIX 10 10 THR B 4 MET B 18 1 15 HELIX 11 11 ASP B 19 TYR B 35 1 17 HELIX 12 12 PRO B 36 SER B 43 5 8 HELIX 13 13 ASN B 57 LYS B 76 1 20 HELIX 14 14 ASN B 80 TYR B 85 1 6 HELIX 15 15 TYR B 85 LYS B 95 1 11 HELIX 16 16 PRO B 100 GLY B 119 1 20 HELIX 17 17 HIS B 120 PHE B 122 5 3 HELIX 18 18 THR B 123 GLY B 142 1 20 LINK FE HEM A 200 NE2 HIS A 88 LINK FE HEM A 200 O HOH 500 LINK FE HEM B 400 NE2 HIS B 63 LINK FE HEM B 400 NE2 HIS B 92 LINK C ACE A 0 N SER A 1 CRYST1 108.516 65.095 55.750 90.00 113.48 90.00 C 1 2 1 4 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 0.009220 0.000000 0.004000 0.00000 SCALE2 0.000000 0.015360 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019560 0.00000