HEADER OXYGEN STORAGE/TRANSPORT 01-APR-99 1CIK TITLE RECOMBINANT SPERM WHALE MYOGLOBIN I99A MUTANT (MET) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (MYOGLOBIN); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PHYSETER CATODON; SOURCE 3 ORGANISM_COMMON: SPERM WHALE; SOURCE 4 ORGANISM_TAXID: 9755; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS OXYGEN TRANSPORT, HEME, MUSCLE PROTEIN, OXYGEN STORAGE-TRANSPORT KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR E.C.LIONG,G.N.PHILLIPS JR. REVDAT 6 09-AUG-23 1CIK 1 REMARK REVDAT 5 03-NOV-21 1CIK 1 REMARK SEQADV LINK REVDAT 4 24-FEB-09 1CIK 1 VERSN REVDAT 3 17-AUG-01 1CIK 1 DBREF REVDAT 2 21-APR-01 1CIK 1 JRNL HEADER SEQADV REMARK REVDAT 1 09-APR-99 1CIK 0 JRNL AUTH E.C.LIONG,Y.DOU,E.E.SCOTT,J.S.OLSON,G.N.PHILLIPS JR. JRNL TITL WATERPROOFING THE HEME POCKET. ROLE OF PROXIMAL AMINO ACID JRNL TITL 2 SIDE CHAINS IN PREVENTING HEMIN LOSS FROM MYOGLOBIN. JRNL REF J.BIOL.CHEM. V. 276 9093 2001 JRNL REFN ISSN 0021-9258 JRNL PMID 11084036 JRNL DOI 10.1074/JBC.M008593200 REMARK 2 REMARK 2 RESOLUTION. 1.70 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 5.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 83.2 REMARK 3 CROSS-VALIDATION METHOD : FREE R 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) : 0.151 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.153 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 11.100 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 2154 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 19394 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.129 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.130 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.170 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 11.200 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 1794 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 15998 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1222 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 48 REMARK 3 SOLVENT ATOMS : 171 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1445.3 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 5784 REMARK 3 NUMBER OF RESTRAINTS : 5420 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 ANGLE DISTANCES (A) : 0.025 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.005 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.055 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.049 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.083 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.079 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 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 1CIK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-APR-99. REMARK 100 THE DEPOSITION ID IS D_1000000777. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAR-98 REMARK 200 TEMPERATURE (KELVIN) : 295 REMARK 200 PH : 9.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : SIEMENS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26136 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 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 (%) : 92.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.03700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: SHELXS REMARK 200 STARTING MODEL: PDB ENTRY 1MBW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.6-3.0 M (NH4)2SO4, 20 MM TRIS, 1 MM REMARK 280 EDTA, PH 9.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 6 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z REMARK 290 6555 X-Y,X,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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 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: 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 31 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 45 NE - CZ - NH1 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 118 NE - CZ - NH2 ANGL. DEV. = -3.4 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 GLN A 152 -153.04 29.36 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 88.2 REMARK 620 3 HEM A 154 NB 90.1 90.2 REMARK 620 4 HEM A 154 NC 92.3 179.4 89.9 REMARK 620 5 HEM A 154 ND 91.9 89.9 178.0 90.0 REMARK 620 6 HOH A 155 O 178.6 92.4 91.2 87.0 86.8 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 156 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 154 DBREF 1CIK A 0 153 UNP P02185 MYG_PHYCA 1 154 SEQADV 1CIK MET A 0 UNP P02185 0 CLONING ARTIFACT SEQADV 1CIK ALA A 99 UNP P02185 ILE 99 ENGINEERED MUTATION SEQADV 1CIK ASN A 122 UNP P02185 ASP 122 ENGINEERED MUTATION SEQRES 1 A 154 MET VAL LEU SER GLU GLY GLU TRP GLN LEU VAL LEU HIS SEQRES 2 A 154 VAL TRP ALA LYS VAL GLU ALA ASP VAL ALA GLY HIS GLY SEQRES 3 A 154 GLN ASP ILE LEU ILE ARG LEU PHE LYS SER HIS PRO GLU SEQRES 4 A 154 THR LEU GLU LYS PHE ASP ARG PHE LYS HIS LEU LYS THR SEQRES 5 A 154 GLU ALA GLU MET LYS ALA SER GLU ASP LEU LYS LYS HIS SEQRES 6 A 154 GLY VAL THR VAL LEU THR ALA LEU GLY ALA ILE LEU LYS SEQRES 7 A 154 LYS LYS GLY HIS HIS GLU ALA GLU LEU LYS PRO LEU ALA SEQRES 8 A 154 GLN SER HIS ALA THR LYS HIS LYS ALA PRO ILE LYS TYR SEQRES 9 A 154 LEU GLU PHE ILE SER GLU ALA ILE ILE HIS VAL LEU HIS SEQRES 10 A 154 SER ARG HIS PRO GLY ASN PHE GLY ALA ASP ALA GLN GLY SEQRES 11 A 154 ALA MET ASN LYS ALA LEU GLU LEU PHE ARG LYS ASP ILE SEQRES 12 A 154 ALA ALA LYS TYR LYS GLU LEU GLY TYR GLN GLY HET SO4 A 156 5 HET HEM A 154 43 HETNAM SO4 SULFATE ION HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 2 SO4 O4 S 2- FORMUL 3 HEM C34 H32 FE N4 O4 FORMUL 4 HOH *171(H2 O) HELIX 1 A GLU A 4 VAL A 17 1 14 HELIX 2 B VAL A 21 SER A 35 1 15 HELIX 3 C PRO A 37 LYS A 42 1 6 HELIX 4 D GLU A 52 ALA A 57 1 6 HELIX 5 E GLU A 59 LYS A 77 1 19 HELIX 6 F GLU A 83 THR A 95 1 13 HELIX 7 G ILE A 101 ARG A 118 1 18 HELIX 8 H ALA A 125 LEU A 149 1 25 LINK NE2 HIS A 93 FE HEM A 154 1555 1555 2.14 LINK FE HEM A 154 O HOH A 155 1555 1555 2.15 SITE 1 AC1 7 SER A 3 GLU A 4 THR A 51 GLU A 52 SITE 2 AC1 7 ALA A 53 HOH A 315 HOH A 357 SITE 1 AC2 19 LYS A 42 PHE A 43 ARG A 45 HIS A 64 SITE 2 AC2 19 THR A 67 LEU A 89 SER A 92 HIS A 93 SITE 3 AC2 19 HIS A 97 ALA A 99 TYR A 103 LEU A 104 SITE 4 AC2 19 HOH A 155 HOH A 244 HOH A 245 HOH A 248 SITE 5 AC2 19 HOH A 268 HOH A 273 HOH A 362 CRYST1 91.497 91.497 45.944 90.00 90.00 120.00 P 6 6 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 0.010929 0.006310 0.000000 0.00000 SCALE2 0.000000 0.012620 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021766 0.00000