HEADER OXYGEN STORAGE/TRANSPORT 25-MAR-07 2EKU TITLE CRYSTAL STRUCTURE OF MYOGLOBIN RECONSTITUTED WITH 7-METHYL-7- TITLE 2 DEPROPIONATEHEMIN 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; SOURCE 5 TISSUE: SKELETAL MUSCLE KEYWDS GLOBIN FOLD, OXYGEN STORAGE-TRANSPORT COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.HARADA,M.MAKINO,H.SUGIMOTO,S.HIROTA,T.MATSUO,Y.SHIRO,Y.HISAEDA, AUTHOR 2 T.HAYASHI REVDAT 5 25-OCT-23 2EKU 1 REMARK LINK REVDAT 4 21-JUL-10 2EKU 1 HETATM REVDAT 3 24-FEB-09 2EKU 1 VERSN REVDAT 2 20-NOV-07 2EKU 1 JRNL REVDAT 1 14-AUG-07 2EKU 0 JRNL AUTH K.HARADA,M.MAKINO,H.SUGIMOTO,S.HIROTA,T.MATSUO,Y.SHIRO, JRNL AUTH 2 Y.HISAEDA,T.HAYASHI JRNL TITL STRUCTURE AND LIGAND BINDING PROPERTIES OF MYOGLOBINS JRNL TITL 2 RECONSTITUTED WITH MONODEPROPIONATED HEME: FUNCTIONAL ROLE JRNL TITL 3 OF EACH HEME PROPIONATE SIDE CHAIN JRNL REF BIOCHEMISTRY V. 46 9406 2007 JRNL REFN ISSN 0006-2960 JRNL PMID 17636874 JRNL DOI 10.1021/BI7007068 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.133 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.127 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1266 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 24010 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.126 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.120 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.186 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 1155 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 22066 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1216 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 54 REMARK 3 SOLVENT ATOMS : 204 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1471.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 7 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 13539 REMARK 3 NUMBER OF RESTRAINTS : 16393 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 ANGLE DISTANCES (A) : 0.027 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.020 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.023 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.055 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.059 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.000 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.004 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.057 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.084 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2EKU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-MAR-07. REMARK 100 THE DEPOSITION ID IS D_1000026788. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-FEB-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL45XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS V REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25369 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05200 REMARK 200 FOR THE DATA SET : 25.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.32000 REMARK 200 FOR SHELL : 6.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1A6K REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.1M AMMONIUM SULFATE, 100MM BIS-TRIS REMARK 280 PROPANE, PH 6.4, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K 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 15.25850 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 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 DISTANCE REMARK 500 OE1 GLN A 152 O HOH A 1333 2.02 REMARK 500 O HOH A 1296 O HOH A 1352 2.12 REMARK 500 REMARK 500 REMARK: NULL 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 ARG A 45 NE - CZ - NH1 ANGL. DEV. = -4.0 DEGREES REMARK 500 ARG A 45 NE - CZ - NH2 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 118 CD - NE - CZ ANGL. DEV. = 12.9 DEGREES REMARK 500 ARG A 118 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 118 NE - CZ - NH2 ANGL. DEV. = -5.2 DEGREES REMARK 500 TYR A 146 CB - CG - CD1 ANGL. DEV. = 3.6 DEGREES REMARK 500 GLY A 153 C - N - CA ANGL. DEV. = 14.2 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 ASP A 20 66.69 -156.20 REMARK 500 PHE A 123 45.24 -142.40 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 7HE A 154 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 93 NE2 REMARK 620 2 7HE A 154 ND 93.5 REMARK 620 3 7HE A 154 NC 90.5 88.3 REMARK 620 4 7HE A 154 NA 92.3 90.8 177.1 REMARK 620 5 7HE A 154 NB 91.4 174.1 88.3 92.4 REMARK 620 6 HOH A1158 O 177.3 85.8 86.9 90.3 89.2 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 1155 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1156 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1157 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 7HE A 154 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2EKT RELATED DB: PDB DBREF 2EKU A 1 153 UNP P02185 MYG_PHYCA 2 154 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 A1155 5 HET SO4 A1156 5 HET SO4 A1157 5 HET 7HE A 154 39 HETNAM SO4 SULFATE ION HETNAM 7HE 7-METHYL-7-DEPROPIONATEHEMIN FORMUL 2 SO4 3(O4 S 2-) FORMUL 5 7HE C32 H30 FE N4 O2 FORMUL 6 HOH *204(H2 O) HELIX 1 1 SER A 3 GLU A 18 1 16 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 SER A 58 1 8 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 7HE A 154 1555 1555 2.06 LINK FE 7HE A 154 O HOH A1158 1555 1555 2.12 CISPEP 1 GLN A 152 GLY A 153 0 1.43 SITE 1 AC1 8 LYS A 34 THR A 51 GLU A 52 HOH A1160 SITE 2 AC1 8 HOH A1162 HOH A1167 HOH A1192 HOH A1278 SITE 1 AC2 6 ARG A 45 LYS A 63 HIS A 64 THR A 67 SITE 2 AC2 6 HIS A 116 HOH A1244 SITE 1 AC3 4 GLN A 26 LYS A 62 HOH A1250 HOH A1300 SITE 1 AC4 15 THR A 39 LYS A 42 PHE A 43 ARG A 45 SITE 2 AC4 15 HIS A 64 THR A 67 LEU A 89 HIS A 93 SITE 3 AC4 15 HIS A 97 ILE A 99 TYR A 103 HOH A1158 SITE 4 AC4 15 HOH A1220 HOH A1244 HOH A1331 CRYST1 63.768 30.517 34.434 90.00 105.59 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 0.015682 0.000000 0.004376 0.00000 SCALE2 0.000000 0.032769 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030150 0.00000