HEADER OXYGEN STORAGE/TRANSPORT 01-AUG-01 1JP8 TITLE SPERM WHALE MET-MYOGLOBIN (ROOM TEMPERATURE; HIGH PRESSURE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYOGLOBIN; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PHYSETER CATODON; SOURCE 3 ORGANISM_COMMON: SPERM WHALE; SOURCE 4 ORGANISM_TAXID: 9755 KEYWDS OXYGEN STORAGE/TRANSPORT, OXYGEN STORAGE-TRANSPORT COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR P.URAYAMA,S.M.GRUNER,G.N.PHILLIPS JR. REVDAT 3 16-AUG-23 1JP8 1 REMARK LINK REVDAT 2 24-FEB-09 1JP8 1 VERSN REVDAT 1 16-JAN-02 1JP8 0 JRNL AUTH P.URAYAMA,G.N.PHILLIPS JR.,S.M.GRUNER JRNL TITL PROBING SUBSTATES IN SPERM WHALE MYOGLOBIN USING JRNL TITL 2 HIGH-PRESSURE CRYSTALLOGRAPHY. JRNL REF STRUCTURE V. 10 51 2002 JRNL REFN ISSN 0969-2126 JRNL PMID 11796110 JRNL DOI 10.1016/S0969-2126(01)00699-2 REMARK 2 REMARK 2 RESOLUTION. 2.30 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 9.14 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 774116.680 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 90.7 REMARK 3 NUMBER OF REFLECTIONS : 5306 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) : 0.165 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.600 REMARK 3 FREE R VALUE TEST SET COUNT : 560 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.44 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 80.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 684 REMARK 3 BIN R VALUE (WORKING SET) : 0.1950 REMARK 3 BIN FREE R VALUE : 0.2940 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 11.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 91 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.031 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1212 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 58 REMARK 3 SOLVENT ATOMS : 66 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.46000 REMARK 3 B22 (A**2) : 2.09000 REMARK 3 B33 (A**2) : 3.36000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.85000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.13 REMARK 3 LOW RESOLUTION CUTOFF (A) : 9.20 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.31 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.24 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.000 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 16.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.020 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.320 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.100 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.230 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.360 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.34 REMARK 3 BSOL : 12.39 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 : PROTEIN.PARAM REMARK 3 PARAMETER FILE 2 : WATER.PARAM REMARK 3 PARAMETER FILE 3 : HEME.PARAM REMARK 3 PARAMETER FILE 4 : SO4.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : HEME.TOP REMARK 3 TOPOLOGY FILE 4 : SO4.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RESIDUE 153 WAS DISORDERED REMARK 4 REMARK 4 1JP8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-AUG-01. REMARK 100 THE DEPOSITION ID IS D_1000014026. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-DEC-97; 10-APR-98 REMARK 200 TEMPERATURE (KELVIN) : 295; 295 REMARK 200 PH : 6 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N; N REMARK 200 RADIATION SOURCE : ROTATING ANODE; ROTATING ANODE REMARK 200 BEAMLINE : NULL; NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU; RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.541; 1.541 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL; SI 111 CHANNEL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR; AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : UCSD MARK II; UCSD MARK II REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5327 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 9.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.1 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 79.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.13800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1VXH REMARK 200 REMARK 200 REMARK: 295K; 150MPA; PH6; KUNDROT-RICHARDS TYPE BERYLLIUM REMARK 200 PRESSURE CELL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, PH 6, BATCH, REMARK 280 TEMPERATURE 298K 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,Y+1/2,-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 15.40000 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 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC 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 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 GLY A 153 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 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A 20 70.21 -155.94 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A 200 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 93 NE2 REMARK 620 2 HEM A 200 NA 90.8 REMARK 620 3 HEM A 200 NB 83.1 89.8 REMARK 620 4 HEM A 200 NC 90.4 178.5 89.3 REMARK 620 5 HEM A 200 ND 98.4 90.2 178.6 90.6 REMARK 620 6 HOH A 309 O 169.1 99.6 93.6 79.2 85.0 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 200 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1JP6 RELATED DB: PDB REMARK 900 SPERM WHALE MET-MYOGLOBIN (ROOM TEMPERATURE; ROOM PRESSURE) REMARK 900 RELATED ID: 1JP9 RELATED DB: PDB REMARK 900 SPERM WHALE MET-MYOGLOBIN (LOW TEMPERATURE; HIGH PRESSURE--SLOW REMARK 900 COOLED (1.7 K/S) TO 77K WHILE UNDER 200MPA) (COMPARED TO 1JPB TO REMARK 900 SHOW REPRODUCIBILITY OF SLOW COOLING TECHNIQUE). REMARK 900 RELATED ID: 1JPB RELATED DB: PDB REMARK 900 SPERM WHALE MET-MYOGLOBIN (LOW TEMPERATURE; HIGH PRESSURE--SLOW REMARK 900 COOLED (1.7 K/S) TO 77K WHILE UNDER 200MPA) (COMPARED TO 1JP9 TO REMARK 900 SHOW REPRODUCIBILITY OF SLOW COOLING TECHNIQUE). DBREF 1JP8 A 1 153 UNP P02185 MYG_PHYCA 1 153 SEQRES 1 A 153 VAL LEU SER GLU GLY GLU TRP GLN LEU VAL LEU HIS VAL SEQRES 2 A 153 TRP ALA LYS VAL GLU ALA ASP VAL ALA GLY HIS GLY GLN SEQRES 3 A 153 ASP ILE LEU ILE ARG LEU PHE LYS SER HIS PRO GLU THR SEQRES 4 A 153 LEU GLU LYS PHE ASP ARG PHE LYS HIS LEU LYS THR GLU SEQRES 5 A 153 ALA GLU MET LYS ALA SER GLU ASP LEU LYS LYS HIS GLY SEQRES 6 A 153 VAL THR VAL LEU THR ALA LEU GLY ALA ILE LEU LYS LYS SEQRES 7 A 153 LYS GLY HIS HIS GLU ALA GLU LEU LYS PRO LEU ALA GLN SEQRES 8 A 153 SER HIS ALA THR LYS HIS LYS ILE PRO ILE LYS TYR LEU SEQRES 9 A 153 GLU PHE ILE SER GLU ALA ILE ILE HIS VAL LEU HIS SER SEQRES 10 A 153 ARG HIS PRO GLY ASP PHE GLY ALA ASP ALA GLN GLY ALA SEQRES 11 A 153 MET ASN LYS ALA LEU GLU LEU PHE ARG LYS ASP ILE ALA SEQRES 12 A 153 ALA LYS TYR LYS GLU LEU GLY TYR GLN GLY HET SO4 A 201 5 HET SO4 A 202 5 HET SO4 A 203 5 HET HEM A 200 43 HETNAM SO4 SULFATE ION HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 2 SO4 3(O4 S 2-) FORMUL 5 HEM C34 H32 FE N4 O4 FORMUL 6 HOH *66(H2 O) HELIX 1 1 SER A 3 ALA A 19 1 17 HELIX 2 2 ASP A 20 HIS A 36 1 17 HELIX 3 3 HIS A 36 GLU A 41 1 6 HELIX 4 4 THR A 51 ALA A 57 1 7 HELIX 5 5 SER A 58 LYS A 77 1 20 HELIX 6 6 HIS A 82 LYS A 96 1 15 HELIX 7 7 PRO A 100 HIS A 119 1 20 HELIX 8 8 PRO A 120 PHE A 123 5 4 HELIX 9 9 GLY A 124 GLY A 150 1 27 LINK NE2 HIS A 93 FE HEM A 200 1555 1555 2.33 LINK FE HEM A 200 O HOH A 309 1555 1555 2.28 SITE 1 AC1 6 LYS A 34 THR A 51 GLU A 52 HOH A 312 SITE 2 AC1 6 HOH A 317 HOH A 320 SITE 1 AC2 5 ARG A 45 LYS A 63 HIS A 64 THR A 67 SITE 2 AC2 5 HIS A 116 SITE 1 AC3 3 HIS A 119 PRO A 120 GLY A 121 SITE 1 AC4 12 LYS A 42 PHE A 43 ARG A 45 VAL A 68 SITE 2 AC4 12 LEU A 89 SER A 92 HIS A 93 HIS A 97 SITE 3 AC4 12 ILE A 99 TYR A 103 HOH A 309 HOH A 310 CRYST1 64.090 30.800 34.570 90.00 105.69 90.00 P 1 21 1 2 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 0.015603 0.000000 0.004383 0.00000 SCALE2 0.000000 0.032468 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030046 0.00000