[Scop | Full Entry | Seq (local cached copy) | More Options ]
HEADER OXYGEN CARRIER 22-FEB-95 1HBH TITLE STRUCTURE OF DEOXYHAEMOGLOBIN OF THE ANTARCTIC FISH TITLE 2 PAGOTHENIA BERNACCHII AND STRUCTURAL BASIS OF THE ROOT TITLE 3 EFFECT COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEMOGLOBIN (DEOXY) (ALPHA CHAIN); COMPND 3 CHAIN: A, C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: HEMOGLOBIN (DEOXY) (BETA CHAIN); COMPND 7 CHAIN: B, D; 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 CARRIER EXPDTA X-RAY DIFFRACTION AUTHOR N.ITO,N.H.KOMIYAMA,G.FERMI REVDAT 1 20-APR-95 1HBH 0 JRNL AUTH N.ITO,N.H.KOMIYAMA,G.FERMI JRNL TITL STRUCTURE OF DEOXYHAEMOGLOBIN OF THE ANTARCTIC JRNL TITL 2 FISH PAGOTHENIA BERNACCHII WITH AN ANALYSIS OF THE JRNL TITL 3 STRUCTURAL BASIS OF THE ROOT EFFECT BY COMPARISON JRNL TITL 4 OF THE LIGANDED AND UNLIGANDED HAEMOGLOBIN JRNL TITL 5 STRUCTURES. JRNL REF J.MOL.BIOL. V. 250 648 1995 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 : PROLSQ, X-PLOR REMARK 3 AUTHORS : KONNERT,HENDRICKSON 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)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 79.0 REMARK 3 NUMBER OF REFLECTIONS : 29393 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 + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : NULL 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 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4484 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 172 REMARK 3 SOLVENT ATOMS : 38 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 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.487 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.283 ; 3.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.091 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.990 ; 4.500 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1HBH 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 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 : 29393 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 10.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 79.0 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: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -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 48.15000 REMARK 290 SMTRY3 2 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 4 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, C, D 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 NE2 HIS D 92 FE HEM D 148 2.11 REMARK 500 O ILE B 55 O HOH 13 2.18 REMARK 500 NE2 HIS C 88 FE HEM C 144 2.19 DBREF 1HBH A 1 142 UNP P80043 HBA_PAGBE 1 142 DBREF 1HBH B 1 146 UNP P80044 HBB_PAGBE 1 146 DBREF 1HBH C 1 142 UNP P80043 HBA_PAGBE 1 142 DBREF 1HBH D 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 SEQRES 1 C 142 SER LEU SER ASP LYS ASP LYS ALA ALA VAL ARG ALA LEU SEQRES 2 C 142 TRP SER LYS ILE GLY LYS SER ALA ASP ALA ILE GLY ASN SEQRES 3 C 142 ASP ALA LEU SER ARG MET ILE VAL VAL TYR PRO GLN THR SEQRES 4 C 142 LYS THR TYR PHE SER HIS TRP PRO ASP VAL THR PRO GLY SEQRES 5 C 142 SER PRO HIS ILE LYS ALA HIS GLY LYS LYS VAL MET GLY SEQRES 6 C 142 GLY ILE ALA LEU ALA VAL SER LYS ILE ASP ASP LEU LYS SEQRES 7 C 142 THR GLY LEU MET GLU LEU SER GLU GLN HIS ALA TYR LYS SEQRES 8 C 142 LEU ARG VAL ASP PRO ALA ASN PHE LYS ILE LEU ASN HIS SEQRES 9 C 142 CYS ILE LEU VAL VAL ILE SER THR MET PHE PRO LYS GLU SEQRES 10 C 142 PHE THR PRO GLU ALA HIS VAL SER LEU ASP LYS PHE LEU SEQRES 11 C 142 SER GLY VAL ALA LEU ALA LEU ALA GLU ARG TYR ARG SEQRES 1 D 146 VAL GLU TRP THR ASP LYS GLU ARG SER ILE ILE SER ASP SEQRES 2 D 146 ILE PHE SER HIS MET ASP TYR ASP ASP ILE GLY PRO LYS SEQRES 3 D 146 ALA LEU SER ARG CYS LEU ILE VAL TYR PRO TRP THR GLN SEQRES 4 D 146 ARG HIS PHE SER GLY PHE GLY ASN LEU TYR ASN ALA GLU SEQRES 5 D 146 ALA ILE ILE GLY ASN ALA ASN VAL ALA ALA HIS GLY ILE SEQRES 6 D 146 LYS VAL LEU HIS GLY LEU ASP ARG GLY VAL LYS ASN MET SEQRES 7 D 146 ASP ASN ILE ALA ALA THR TYR ALA ASP LEU SER THR LEU SEQRES 8 D 146 HIS SER GLU LYS LEU HIS VAL ASP PRO ASP ASN PHE LYS SEQRES 9 D 146 LEU LEU SER ASP CYS ILE THR ILE VAL LEU ALA ALA LYS SEQRES 10 D 146 MET GLY HIS ALA PHE THR ALA GLU THR GLN GLY ALA PHE SEQRES 11 D 146 GLN LYS PHE LEU ALA VAL VAL VAL SER ALA LEU GLY LYS SEQRES 12 D 146 GLN TYR HIS HET ACE A 0 3 HET ACE C 0 3 HET HEM A 144 43 HET HEM B 148 43 HET HEM C 144 43 HET HEM D 148 43 HETNAM ACE ACETYL GROUP HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 5 ACE 2(C2 H4 O) FORMUL 7 HEM 4(C34 H32 FE N4 O4) FORMUL 11 HOH *38(H2 O) HELIX 1 1 ASP A 4 VAL A 35 1 32 HELIX 2 2 PRO A 37 PHE A 43 5 7 HELIX 3 3 PRO A 54 SER A 72 1 19 HELIX 4 4 LEU A 77 GLY A 80 1 4 HELIX 5 5 MET A 82 TYR A 90 1 9 HELIX 6 6 PRO A 96 MET A 113 5 18 HELIX 7 7 PRO A 120 LEU A 137 1 18 HELIX 8 8 ASP B 5 HIS B 17 1 13 HELIX 9 9 TYR B 20 VAL B 34 1 15 HELIX 10 10 PRO B 36 HIS B 41 5 6 HELIX 11 11 ALA B 51 GLY B 56 1 6 HELIX 12 12 ALA B 58 LYS B 76 1 19 HELIX 13 13 ILE B 81 GLU B 94 1 14 HELIX 14 14 PRO B 100 ALA B 121 5 22 HELIX 15 15 ALA B 124 GLY B 142 1 19 HELIX 16 16 ASP C 4 VAL C 35 1 32 HELIX 17 17 PRO C 37 PHE C 43 5 7 HELIX 18 18 PRO C 54 SER C 72 1 19 HELIX 19 19 LEU C 77 GLY C 80 1 4 HELIX 20 20 MET C 82 ALA C 89 1 8 HELIX 21 21 PRO C 96 MET C 113 5 18 HELIX 22 22 PRO C 120 LEU C 137 1 18 HELIX 23 23 ASP D 5 SER D 16 1 12 HELIX 24 24 TYR D 20 VAL D 34 1 15 HELIX 25 25 PRO D 36 HIS D 41 5 6 HELIX 26 26 ALA D 51 GLY D 56 1 6 HELIX 27 27 ALA D 58 LYS D 76 1 19 HELIX 28 28 ILE D 81 GLU D 94 1 14 HELIX 29 29 ASP D 101 ALA D 121 1 21 HELIX 30 30 ALA D 124 GLY D 142 1 19 LINK C ACE A 0 N SER A 1 LINK C ACE C 0 N SER C 1 CRYST1 62.650 96.300 62.650 90.00 90.00 90.00 P 1 21 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 0.015962 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010384 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015962 0.00000 MTRIX1 1 -0.002580 -0.001140 -1.000000 5.73624 1 MTRIX2 1 0.011650 -0.999930 0.001110 -2.20982 1 MTRIX3 1 -0.999930 -0.011650 0.002590 5.73214 1