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HEADER OXYGEN TRANSPORT 04-NOV-91 1PBX TITLE HAEMOGLOBIN OF THE ANTARCTIC FISH PAGOTHENIA BERNACCHII: TITLE 2 AMINO ACID SEQUENCE, OXYGEN EQUILIBRIA AND CRYSTAL TITLE 3 STRUCTURE OF ITS CARBONMONOXY DERIVATIVE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEMOGLOBIN (CARBONMONOXY) (ALPHA CHAIN); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: HEMOGLOBIN (CARBONMONOXY) (BETA CHAIN); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PAGOTHENIA BERNACCHII; SOURCE 3 MOL_ID: 2; SOURCE 4 ORGANISM_SCIENTIFIC: PAGOTHENIA BERNACCHII KEYWDS OXYGEN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR G.FERMI REVDAT 2 01-APR-03 1PBX 1 JRNL REVDAT 1 15-OCT-92 1PBX 0 JRNL AUTH L.CAMARDELLA,C.CARUSO,R.D'AVINO,G.DI PRISCO, JRNL AUTH 2 B.RUTIGLIANO,M.TAMBURRINI,G.FERMI,M.F.PERUTZ JRNL TITL HAEMOGLOBIN OF THE ANTARCTIC FISH PAGOTHENIA JRNL TITL 2 BERNACCHII. AMINO ACID SEQUENCE, OXYGEN EQUILIBRIA JRNL TITL 3 AND CRYSTAL STRUCTURE OF ITS CARBONMONOXY JRNL TITL 4 DERIVATIVE. JRNL REF J.MOL.BIOL. V. 224 449 1992 JRNL REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL 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 : 13785 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) : 0.178 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL 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 : 2242 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 90 REMARK 3 SOLVENT ATOMS : 28 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) : 0.019 REMARK 3 BOND ANGLES (DEGREES) : 2.00 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 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 1PBX 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 (2007-03-23) REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL 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) : 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: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 45.69000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.27000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 45.69000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 44.27000 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 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 NE2 HIS A 88 FE HEM A 144 2.14 REMARK 500 NE2 HIS B 92 FE HEM B 148 2.15 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 SER A 1 113.48 102.22 DBREF 1PBX A 1 142 UNP P80043 HBA_PAGBE 1 142 DBREF 1PBX B 1 146 UNP P80044 HBB_PAGBE 1 146 SEQRES 1 A 143 ACE SER LEU SER ASP LYS ASP LYS ALA ALA VAL ARG ALA SEQRES 2 A 143 LEU TRP SER LYS ILE GLY LYS SER ALA ASP ALA ILE GLY SEQRES 3 A 143 ASN ASP ALA LEU SER ARG MET ILE VAL VAL TYR PRO GLN SEQRES 4 A 143 THR LYS THR TYR PHE SER HIS TRP PRO ASP VAL THR PRO SEQRES 5 A 143 GLY SER PRO HIS ILE LYS ALA HIS GLY LYS LYS VAL MET SEQRES 6 A 143 GLY GLY ILE ALA LEU ALA VAL SER LYS ILE ASP ASP LEU SEQRES 7 A 143 LYS THR GLY LEU MET GLU LEU SER GLU GLN HIS ALA TYR SEQRES 8 A 143 LYS LEU ARG VAL ASP PRO ALA ASN PHE LYS ILE LEU ASN SEQRES 9 A 143 HIS CYS ILE LEU VAL VAL ILE SER THR MET PHE PRO LYS SEQRES 10 A 143 GLU PHE THR PRO GLU ALA HIS VAL SER LEU ASP LYS PHE SEQRES 11 A 143 LEU 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 144 43 HET CMO A 145 2 HET HEM B 148 43 HET CMO B 149 2 HETNAM ACE ACETYL GROUP HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM CMO CARBON MONOXIDE HETSYN HEM HEME FORMUL 1 ACE C2 H4 O FORMUL 3 HEM 2(C34 H32 FE N4 O4) FORMUL 4 CMO 2(C O) FORMUL 7 HOH *28(H2 O) HELIX 1 AA SER A 3 GLY A 18 1 16 HELIX 2 BA SER A 20 VAL A 35 1 16 HELIX 3 CA TYR A 36 TYR A 42 1 7 HELIX 4 EA SER A 53 SER A 72 1 20 HELIX 5 FA LEU A 81 ALA A 89 1 9 HELIX 6 GA ASP A 95 MET A 113 1 19 HELIX 7 HA THR A 119 GLU A 139 1 21 HELIX 8 AB THR B 4 MET B 18 1 15 HELIX 9 BB ASP B 19 VAL B 34 1 16 HELIX 10 CB TYR B 35 HIS B 41 1 7 HELIX 11 DB ASN B 50 GLY B 56 1 7 HELIX 12 EB ASN B 57 LYS B 76 1 20 HELIX 13 FB TYR B 85 SER B 93 1 9 HELIX 14 GB ASP B 99 LYS B 117 1 19 HELIX 15 HB THR B 123 LYS B 143 1 21 LINK C CMO A 145 FE HEM A 144 LINK C CMO B 149 FE HEM B 148 SITE 1 STA 2 HIS A 88 HEM A 144 SITE 1 STB 2 HIS B 92 HEM B 148 CRYST1 91.380 88.540 55.340 90.00 97.16 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 0.010943 0.000000 0.001375 0.00000 SCALE2 0.000000 0.011294 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018212 0.00000