HEADER OXYGEN TRANSPORT 02-DEC-94 1MYF TITLE SOLUTION STRUCTURE OF CARBONMONOXY MYOGLOBIN DETERMINED FROM NMR TITLE 2 DISTANCE AND CHEMICAL SHIFT CONSTRAINTS COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYOGLOBIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PHYSETER CATODON; SOURCE 3 ORGANISM_COMMON: SPERM WHALE; SOURCE 4 ORGANISM_TAXID: 9755 KEYWDS OXYGEN TRANSPORT EXPDTA SOLUTION NMR NUMMDL 12 AUTHOR K.OSAPAY,Y.THERIAULT,P.E.WRIGHT,D.A.CASE REVDAT 4 23-FEB-22 1MYF 1 REMARK LINK REVDAT 3 24-FEB-09 1MYF 1 VERSN REVDAT 2 01-APR-03 1MYF 1 JRNL REVDAT 1 27-FEB-95 1MYF 0 JRNL AUTH K.OSAPAY,Y.THERIAULT,P.E.WRIGHT,D.A.CASE JRNL TITL SOLUTION STRUCTURE OF CARBONMONOXY MYOGLOBIN DETERMINED FROM JRNL TITL 2 NUCLEAR MAGNETIC RESONANCE DISTANCE AND CHEMICAL SHIFT JRNL TITL 3 CONSTRAINTS. JRNL REF J.MOL.BIOL. V. 244 183 1994 JRNL REFN ISSN 0022-2836 JRNL PMID 7966330 JRNL DOI 10.1006/JMBI.1994.1718 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH G.P.GIPPERT,P.F.YIP,P.E.WRIGHT,D.A.CASE REMARK 1 TITL COMPUTATIONAL METHODS FOR DETERMINING PROTEIN STRUCTURES REMARK 1 TITL 2 FROM NMR DATA REMARK 1 REF BIOCHEM.PHARM. V. 40 15 1990 REMARK 1 REFN ISSN 0006-2952 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : HAVEL,WUTHRICH (DISGEO), REMARK 3 PEARLMAN,CASE,CALDWELL,SEIBEL,SINGH,WEINER,KOLLMAN REMARK 3 (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1MYF COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000175185. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : NULL REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : NULL REMARK 210 SPECTROMETER MODEL : NULL REMARK 210 SPECTROMETER MANUFACTURER : NULL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 12 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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 PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 1 VAL A 68 CA - CB - CG1 ANGL. DEV. = 10.2 DEGREES REMARK 500 1 HIS A 82 CB - CA - C ANGL. DEV. = 12.5 DEGREES REMARK 500 1 TYR A 103 CB - CG - CD2 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 TYR A 146 CB - CG - CD2 ANGL. DEV. = -4.3 DEGREES REMARK 500 2 VAL A 68 CA - CB - CG1 ANGL. DEV. = 9.4 DEGREES REMARK 500 2 TYR A 103 CB - CG - CD2 ANGL. DEV. = -3.9 DEGREES REMARK 500 3 TYR A 146 CB - CG - CD2 ANGL. DEV. = -3.7 DEGREES REMARK 500 4 VAL A 68 CA - CB - CG1 ANGL. DEV. = 9.6 DEGREES REMARK 500 5 VAL A 68 CA - CB - CG1 ANGL. DEV. = 9.3 DEGREES REMARK 500 6 VAL A 68 CA - CB - CG1 ANGL. DEV. = 10.3 DEGREES REMARK 500 6 TYR A 151 CB - CG - CD1 ANGL. DEV. = -3.8 DEGREES REMARK 500 7 HIS A 48 CB - CG - CD2 ANGL. DEV. = -13.3 DEGREES REMARK 500 7 VAL A 68 CA - CB - CG1 ANGL. DEV. = 9.3 DEGREES REMARK 500 7 PRO A 88 C - N - CA ANGL. DEV. = 9.6 DEGREES REMARK 500 8 TYR A 103 CB - CG - CD2 ANGL. DEV. = -4.7 DEGREES REMARK 500 9 VAL A 68 CA - CB - CG1 ANGL. DEV. = 10.0 DEGREES REMARK 500 10 VAL A 68 CA - CB - CG1 ANGL. DEV. = 10.6 DEGREES REMARK 500 11 VAL A 68 CA - CB - CG1 ANGL. DEV. = 10.2 DEGREES REMARK 500 11 TYR A 103 CB - CG - CD2 ANGL. DEV. = -4.0 DEGREES REMARK 500 11 TYR A 146 CB - CG - CD2 ANGL. DEV. = -3.8 DEGREES REMARK 500 12 HIS A 48 CB - CG - CD2 ANGL. DEV. = -13.3 DEGREES REMARK 500 12 VAL A 68 CA - CB - CG1 ANGL. DEV. = 9.4 DEGREES REMARK 500 12 PRO A 88 C - N - CA ANGL. DEV. = 9.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 1 GLU A 52 62.65 35.06 REMARK 500 1 ALA A 53 103.53 73.04 REMARK 500 1 GLU A 54 42.98 -75.53 REMARK 500 1 LYS A 56 -83.98 -141.48 REMARK 500 1 ALA A 57 55.86 32.08 REMARK 500 1 GLU A 59 -72.19 65.05 REMARK 500 1 LYS A 79 55.27 33.75 REMARK 500 1 HIS A 82 65.38 -13.07 REMARK 500 1 ALA A 84 -23.37 70.03 REMARK 500 1 GLU A 85 -66.09 -146.35 REMARK 500 1 LEU A 86 -50.04 74.21 REMARK 500 1 LYS A 87 -56.92 -26.37 REMARK 500 1 LYS A 98 54.84 97.47 REMARK 500 1 ILE A 99 -100.97 40.93 REMARK 500 1 LYS A 102 -74.81 33.62 REMARK 500 1 TYR A 151 -64.46 -125.58 REMARK 500 2 HIS A 81 61.74 -117.03 REMARK 500 2 ALA A 94 -63.39 -93.12 REMARK 500 2 ASP A 122 -49.25 -165.23 REMARK 500 2 GLN A 152 -50.98 67.15 REMARK 500 3 GLU A 18 37.50 106.45 REMARK 500 3 ALA A 19 24.86 45.04 REMARK 500 3 ASP A 20 54.12 -94.04 REMARK 500 3 THR A 51 -160.76 -161.54 REMARK 500 3 ALA A 53 -45.72 81.14 REMARK 500 3 HIS A 81 56.24 -107.69 REMARK 500 3 GLU A 83 -48.06 174.30 REMARK 500 3 ALA A 94 -79.29 -72.59 REMARK 500 3 LYS A 98 -54.85 -172.89 REMARK 500 3 ILE A 99 -75.72 108.63 REMARK 500 4 SER A 3 -177.01 -170.48 REMARK 500 4 SER A 35 -72.03 -64.29 REMARK 500 4 PRO A 37 -21.02 -35.40 REMARK 500 4 GLU A 52 77.05 -65.89 REMARK 500 4 ALA A 53 -50.19 -163.54 REMARK 500 4 HIS A 81 66.05 -114.18 REMARK 500 4 HIS A 82 -100.28 -112.87 REMARK 500 4 GLU A 83 -40.27 74.12 REMARK 500 4 ALA A 94 -71.39 -76.23 REMARK 500 4 LYS A 98 82.82 75.71 REMARK 500 4 ILE A 99 -84.61 18.79 REMARK 500 4 PRO A 100 102.96 -22.66 REMARK 500 4 ASP A 122 -44.36 -160.70 REMARK 500 5 GLU A 38 -44.48 -143.80 REMARK 500 5 ASP A 44 -67.97 68.01 REMARK 500 5 ARG A 45 34.63 -161.98 REMARK 500 5 LYS A 47 -1.52 35.26 REMARK 500 5 HIS A 48 -2.25 -172.81 REMARK 500 5 LYS A 50 -60.85 -151.68 REMARK 500 5 SER A 58 84.82 -68.85 REMARK 500 REMARK 500 THIS ENTRY HAS 142 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 HIS A 81 0.08 SIDE CHAIN REMARK 500 1 TYR A 103 0.16 SIDE CHAIN REMARK 500 1 PHE A 106 0.08 SIDE CHAIN REMARK 500 1 HIS A 116 0.09 SIDE CHAIN REMARK 500 2 TYR A 103 0.07 SIDE CHAIN REMARK 500 2 HIS A 116 0.08 SIDE CHAIN REMARK 500 3 PHE A 46 0.11 SIDE CHAIN REMARK 500 3 TYR A 103 0.14 SIDE CHAIN REMARK 500 3 PHE A 106 0.07 SIDE CHAIN REMARK 500 3 HIS A 119 0.10 SIDE CHAIN REMARK 500 3 TYR A 151 0.12 SIDE CHAIN REMARK 500 4 PHE A 46 0.08 SIDE CHAIN REMARK 500 4 TYR A 103 0.08 SIDE CHAIN REMARK 500 4 PHE A 106 0.09 SIDE CHAIN REMARK 500 4 TYR A 151 0.08 SIDE CHAIN REMARK 500 5 PHE A 46 0.10 SIDE CHAIN REMARK 500 5 HIS A 48 0.12 SIDE CHAIN REMARK 500 5 TYR A 103 0.16 SIDE CHAIN REMARK 500 6 TYR A 103 0.15 SIDE CHAIN REMARK 500 6 TYR A 151 0.17 SIDE CHAIN REMARK 500 7 PHE A 46 0.13 SIDE CHAIN REMARK 500 7 HIS A 48 0.25 SIDE CHAIN REMARK 500 7 TYR A 103 0.11 SIDE CHAIN REMARK 500 7 PHE A 106 0.09 SIDE CHAIN REMARK 500 8 TYR A 103 0.08 SIDE CHAIN REMARK 500 8 HIS A 113 0.10 SIDE CHAIN REMARK 500 8 HIS A 119 0.09 SIDE CHAIN REMARK 500 9 PHE A 46 0.08 SIDE CHAIN REMARK 500 9 TYR A 103 0.15 SIDE CHAIN REMARK 500 10 PHE A 46 0.12 SIDE CHAIN REMARK 500 10 PHE A 106 0.10 SIDE CHAIN REMARK 500 10 HIS A 113 0.11 SIDE CHAIN REMARK 500 11 PHE A 46 0.11 SIDE CHAIN REMARK 500 11 HIS A 48 0.12 SIDE CHAIN REMARK 500 11 TYR A 103 0.10 SIDE CHAIN REMARK 500 11 ARG A 118 0.10 SIDE CHAIN REMARK 500 11 PHE A 138 0.09 SIDE CHAIN REMARK 500 12 PHE A 46 0.13 SIDE CHAIN REMARK 500 12 HIS A 48 0.25 SIDE CHAIN REMARK 500 12 TYR A 103 0.11 SIDE CHAIN REMARK 500 12 PHE A 106 0.09 SIDE CHAIN 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 154 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 93 NE2 REMARK 620 2 HEM A 154 NA 91.1 REMARK 620 3 HEM A 154 NB 87.1 88.6 REMARK 620 4 HEM A 154 NC 93.5 175.3 91.1 REMARK 620 5 HEM A 154 ND 91.9 90.5 178.6 89.9 REMARK 620 6 CMO A 155 C 175.5 93.3 93.2 82.0 87.9 REMARK 620 7 CMO A 155 O 173.9 95.0 93.8 80.4 87.3 1.7 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 154 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CMO A 155 DBREF 1MYF 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 HEM A 154 73 HET CMO A 155 2 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM CMO CARBON MONOXIDE HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 CMO C O HELIX 1 1 GLU A 4 SER A 35 1 32 HELIX 2 2 PRO A 37 LYS A 42 1 6 HELIX 3 3 ASP A 44 LYS A 47 1 4 HELIX 4 4 ASP A 60 LYS A 77 1 18 HELIX 5 5 LYS A 87 THR A 95 1 9 HELIX 6 6 ILE A 101 ARG A 118 5 18 HELIX 7 7 ALA A 125 GLU A 148 1 24 LINK NE2 HIS A 93 FE HEM A 154 1555 1555 2.01 LINK FE HEM A 154 C CMO A 155 1555 1555 1.74 LINK FE HEM A 154 O CMO A 155 1555 1555 2.86 SITE 1 AC1 14 THR A 39 PHE A 43 ARG A 45 HIS A 64 SITE 2 AC1 14 THR A 67 VAL A 68 LEU A 72 SER A 92 SITE 3 AC1 14 HIS A 93 HIS A 97 TYR A 103 LEU A 104 SITE 4 AC1 14 ILE A 107 CMO A 155 SITE 1 AC2 4 PHE A 43 HIS A 64 VAL A 68 HEM A 154 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1