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HEADER OXYGEN STORAGE/TRANSPORT 05-JAN-02 1IT2 TITLE HAGFISH DEOXY HEMOGLOBIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEMOGLOBIN; COMPND 3 CHAIN: A, B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: EPTATRETUS BURGERI; SOURCE 3 ORGANISM_COMMON: INSHORE HAGFISH KEYWDS HAGFISH, EPTATRETUS BURGERI, DEOXY FORM EXPDTA X-RAY DIFFRACTION AUTHOR M.MITO,K.T.CHONG,S.-Y.PARK,J.R.TAME REVDAT 2 17-JUN-03 1IT2 1 JRNL REVDAT 1 23-JAN-02 1IT2 0 JRNL AUTH M.MITO,K.T.CHONG,G.MIYAZAKI,S.ADACHI,S.-Y.PARK, JRNL AUTH 2 J.R.TAME,H.MORIMOTO JRNL TITL CRYSTAL STRUCTURES OF DEOXY- AND JRNL TITL 2 CARBONMONOXYHEMOGLOBIN F1 FROM THE HAGFISH JRNL TITL 3 EPTATRETUS BURGERI JRNL REF J.BIOL.CHEM. V. 277 21898 2002 JRNL REFN ASTM JBCHA3 US ISSN 0021-9258 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 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) (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 52897 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 2687 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.70 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3230 REMARK 3 BIN FREE R VALUE : 0.3250 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 416 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.016 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2380 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 86 REMARK 3 SOLVENT ATOMS : 392 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) : 0.20 REMARK 3 ESD FROM SIGMAA (A) : 0.20 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.20 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.18 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.10 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.83 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC 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 1IT2 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 RCSB005251. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-OCT-2000 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI111 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52908 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 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 (%) : 99.2 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.29100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: PDB ENTRY 1F5O REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, TRIS-BUFFER, PH 6.5, REMARK 280 SMALL TUBES, TEMPERATURE 298K 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 52.01200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.13450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 52.01200 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 31.13450 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH 2 LIES ON A SPECIAL POSITION. 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 HIS A 103 CG HIS A 103 CD2 0.050 REMARK 500 PRO B 201 CB PRO B 201 CG 0.043 REMARK 500 HIS B 303 CG HIS B 303 CD2 0.055 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 TRP A 23 N - CA - C ANGL. DEV. = 8.5 DEGREES REMARK 500 SER A 144 N - CA - C ANGL. DEV. = 6.5 DEGREES REMARK 500 TRP B 223 N - CA - C ANGL. DEV. = 6.6 DEGREES 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 60 141.66 70.11 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1IT3 RELATED DB: PDB REMARK 900 1IT3 CONTAINS HAGFISH CO LIGAND HEMOGLOBIN DBREF 1IT2 A 1 146 UNP Q7SID0 Q7SID0_EPTBU 1 146 DBREF 1IT2 B 201 346 UNP Q7SID0 Q7SID0_EPTBU 1 146 SEQRES 1 A 146 PRO ILE ILE ASP GLN GLY PRO LEU PRO THR LEU THR ASP SEQRES 2 A 146 GLY ASP LYS LYS ALA ILE ASN LYS ILE TRP PRO LYS ILE SEQRES 3 A 146 TYR LYS GLU TYR GLU GLN TYR SER LEU ASN ILE LEU LEU SEQRES 4 A 146 ARG PHE LEU LYS CYS PHE PRO GLN ALA GLN ALA SER PHE SEQRES 5 A 146 PRO LYS PHE SER THR LYS LYS SER ASN LEU GLU GLN ASP SEQRES 6 A 146 PRO GLU VAL LYS HIS GLN ALA VAL VAL ILE PHE ASN LYS SEQRES 7 A 146 VAL ASN GLU ILE ILE ASN SER MET ASP ASN GLN GLU GLU SEQRES 8 A 146 ILE ILE LYS SER LEU LYS ASP LEU SER GLN LYS HIS LYS SEQRES 9 A 146 THR VAL PHE LYS VAL ASP SER ILE TRP PHE LYS GLU LEU SEQRES 10 A 146 SER SER ILE PHE VAL SER THR ILE ASP GLY GLY ALA GLU SEQRES 11 A 146 PHE GLU LYS LEU PHE SER ILE ILE CYS ILE LEU LEU ARG SEQRES 12 A 146 SER ALA TYR SEQRES 1 B 146 PRO ILE ILE ASP GLN GLY PRO LEU PRO THR LEU THR ASP SEQRES 2 B 146 GLY ASP LYS LYS ALA ILE ASN LYS ILE TRP PRO LYS ILE SEQRES 3 B 146 TYR LYS GLU TYR GLU GLN TYR SER LEU ASN ILE LEU LEU SEQRES 4 B 146 ARG PHE LEU LYS CYS PHE PRO GLN ALA GLN ALA SER PHE SEQRES 5 B 146 PRO LYS PHE SER THR LYS LYS SER ASN LEU GLU GLN ASP SEQRES 6 B 146 PRO GLU VAL LYS HIS GLN ALA VAL VAL ILE PHE ASN LYS SEQRES 7 B 146 VAL ASN GLU ILE ILE ASN SER MET ASP ASN GLN GLU GLU SEQRES 8 B 146 ILE ILE LYS SER LEU LYS ASP LEU SER GLN LYS HIS LYS SEQRES 9 B 146 THR VAL PHE LYS VAL ASP SER ILE TRP PHE LYS GLU LEU SEQRES 10 B 146 SER SER ILE PHE VAL SER THR ILE ASP GLY GLY ALA GLU SEQRES 11 B 146 PHE GLU LYS LEU PHE SER ILE ILE CYS ILE LEU LEU ARG SEQRES 12 B 146 SER ALA TYR HET HEM A 147 43 HET HEM B 347 43 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 3 HEM 2(C34 H32 FE N4 O4) FORMUL 5 HOH *392(H2 O) HELIX 1 1 THR A 12 LYS A 28 1 17 HELIX 2 2 GLU A 29 PHE A 45 1 17 HELIX 3 3 PRO A 46 PHE A 52 5 7 HELIX 4 4 ASN A 61 GLN A 64 5 4 HELIX 5 5 ASP A 65 ASN A 84 1 20 HELIX 6 6 ASN A 88 VAL A 106 1 19 HELIX 7 7 ILE A 112 ILE A 125 1 14 HELIX 8 8 GLY A 128 SER A 144 1 17 HELIX 9 9 THR B 212 LYS B 228 1 17 HELIX 10 10 GLU B 229 PHE B 245 1 17 HELIX 11 11 PRO B 246 PHE B 252 5 7 HELIX 12 12 ASN B 261 GLN B 264 5 4 HELIX 13 13 ASP B 265 SER B 285 1 21 HELIX 14 14 ASN B 288 VAL B 306 1 19 HELIX 15 15 ILE B 312 ILE B 325 1 14 HELIX 16 16 GLY B 328 ARG B 343 1 16 CRYST1 104.024 62.269 66.536 90.00 107.40 90.00 C 1 2 1 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 0.009613 0.000000 0.003012 0.00000 SCALE2 0.000000 0.016059 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015750 0.00000