HEADER OXYGEN TRANSPORT 20-JUN-96 1RSE TITLE MYOGLOBIN (HORSE HEART) MUTANT WITH SER 92 REPLACED BY ASP (S92D) COMPND MOL_ID: 1; COMPND 2 MOLECULE: HORSE HEART MYOGLOBIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: EQUUS CABALLUS; SOURCE 3 ORGANISM_COMMON: HORSE; SOURCE 4 ORGANISM_TAXID: 9796; SOURCE 5 ORGAN: HEART; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HEME, OXYGEN TRANSPORT, RESPIRATORY PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR D.L.BURK,G.D.BRAYER REVDAT 4 14-FEB-24 1RSE 1 REMARK REVDAT 3 03-NOV-21 1RSE 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 1RSE 1 VERSN REVDAT 1 23-DEC-96 1RSE 0 JRNL AUTH E.LLOYD,D.L.BURK,J.C.FERRER,R.MAURUS,J.DORAN,P.R.CAREY, JRNL AUTH 2 G.D.BRAYER,A.G.MAUK JRNL TITL ELECTROSTATIC MODIFICATION OF THE ACTIVE SITE OF MYOGLOBIN: JRNL TITL 2 CHARACTERIZATION OF THE PROXIMAL SER92ASP VARIANT. JRNL REF BIOCHEMISTRY V. 35 11901 1996 JRNL REFN ISSN 0006-2960 JRNL PMID 8794773 JRNL DOI 10.1021/BI9608976 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.G.GUILLEMETTE,Y.MATSUSHIMA-HIBIYA,T.ATKINSON,M.SMITH REMARK 1 TITL EXPRESSION IN ESCHERICHIA COLI OF A SYNTHETIC GENE CODING REMARK 1 TITL 2 FOR HORSE HEART MYOGLOBIN REMARK 1 REF PROTEIN ENG. V. 4 585 1991 REMARK 1 REFN ISSN 0269-2139 REMARK 1 REFERENCE 2 REMARK 1 AUTH S.V.EVANS,G.D.BRAYER REMARK 1 TITL HIGH-RESOLUTION STUDY OF THE THREE-DIMENSIONAL STRUCTURE OF REMARK 1 TITL 2 HORSE HEART METMYOGLOBIN REMARK 1 REF J.MOL.BIOL. V. 213 885 1990 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 3 REMARK 1 AUTH S.V.EVANS,G.D.BRAYER REMARK 1 TITL HORSE HEART METMYOGLOBIN. A 2.8-A RESOLUTION REMARK 1 TITL 2 THREE-DIMENSIONAL STRUCTURE DETERMINATION REMARK 1 REF J.BIOL.CHEM. V. 263 4263 1988 REMARK 1 REFN ISSN 0021-9258 REMARK 1 REFERENCE 4 REMARK 1 AUTH C.SHERWOOD,A.G.MAUK,G.D.BRAYER REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY DIFFRACTION DATA FOR HORSE REMARK 1 TITL 2 HEART METMYOGLOBIN REMARK 1 REF J.MOL.BIOL. V. 193 227 1987 REMARK 1 REFN ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROLSQ REMARK 3 AUTHORS : KONNERT,HENDRICKSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 11615 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.1880 REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 11615 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1201 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 48 REMARK 3 SOLVENT ATOMS : 61 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.80 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.015 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.031 ; 0.030 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.046 ; 0.050 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.010 ; 0.020 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.048 ; 0.060 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.193 ; 0.200 REMARK 3 MULTIPLE TORSION (A) : 0.159 ; 0.200 REMARK 3 H-BOND (X...Y) (A) : 0.147 ; 0.200 REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : 1.300 ; 1.500 REMARK 3 STAGGERED (DEGREES) : 17.800; 20.000 REMARK 3 TRANSVERSE (DEGREES) : 37.000; 15.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.376 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.107 ; 2.500 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.361 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.769 ; 3.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1RSE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000176198. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-MAY-93 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL 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 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : OSCILL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11967 REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 85.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : NULL REMARK 200 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 14.44000 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: 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. = 4.2 DEGREES REMARK 500 LYS A 77 CA - CB - CG ANGL. DEV. = 17.4 DEGREES REMARK 500 ARG A 139 CD - NE - CZ ANGL. DEV. = 9.8 DEGREES REMARK 500 ASP A 141 CB - CG - OD1 ANGL. DEV. = 7.6 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 73.29 -151.00 REMARK 500 LYS A 50 -62.07 -96.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 HOH 156 IS COVALENTLY BOUND TO THE IRON OF THE HEME. 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 94.8 REMARK 620 3 HEM A 154 NB 91.0 89.8 REMARK 620 4 HEM A 154 NC 87.4 177.2 88.3 REMARK 620 5 HEM A 154 ND 91.9 90.1 177.1 91.7 REMARK 620 6 HOH A 156 O 170.0 95.2 89.4 82.7 87.7 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 155 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 154 DBREF 1RSE A 1 153 UNP P68082 MYG_HORSE 1 153 SEQADV 1RSE ASP A 92 UNP P68082 SER 92 ENGINEERED MUTATION SEQRES 1 A 153 GLY LEU SER ASP GLY GLU TRP GLN GLN VAL LEU ASN VAL SEQRES 2 A 153 TRP GLY LYS VAL GLU ALA ASP ILE ALA GLY HIS GLY GLN SEQRES 3 A 153 GLU VAL LEU ILE ARG LEU PHE THR GLY HIS PRO GLU THR SEQRES 4 A 153 LEU GLU LYS PHE ASP LYS 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 THR VAL VAL LEU THR ALA LEU GLY GLY 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 ASP HIS ALA THR LYS HIS LYS ILE PRO ILE LYS TYR LEU SEQRES 9 A 153 GLU PHE ILE SER ASP ALA ILE ILE HIS VAL LEU HIS SER SEQRES 10 A 153 LYS HIS PRO GLY ASP PHE GLY ALA ASP ALA GLN GLY ALA SEQRES 11 A 153 MET THR LYS ALA LEU GLU LEU PHE ARG ASN ASP ILE ALA SEQRES 12 A 153 ALA LYS TYR LYS GLU LEU GLY PHE GLN GLY HET SO4 A 155 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 *61(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 PHE A 43 5 8 HELIX 4 4 THR A 51 SER A 58 1 8 HELIX 5 5 SER A 58 LYS A 79 1 22 HELIX 6 6 HIS A 82 HIS A 97 1 16 HELIX 7 7 PRO A 100 HIS A 119 1 20 HELIX 8 8 GLY A 124 GLY A 150 1 27 LINK NE2 HIS A 93 FE HEM A 154 1555 1555 2.10 LINK FE HEM A 154 O HOH A 156 1555 1555 2.31 SITE 1 AC1 5 SER A 58 GLU A 59 ASP A 60 HOH A 177 SITE 2 AC1 5 HOH A 207 SITE 1 AC2 17 THR A 39 LYS A 42 PHE A 43 LYS A 45 SITE 2 AC2 17 VAL A 68 HIS A 93 LYS A 96 HIS A 97 SITE 3 AC2 17 ILE A 99 TYR A 103 LEU A 104 HIS A 113 SITE 4 AC2 17 HIS A 116 GLN A 128 HOH A 156 HOH A 209 SITE 5 AC2 17 HOH A 215 CRYST1 64.420 28.880 35.970 90.00 107.00 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 0.015523 0.000000 0.004746 0.00000 SCALE2 0.000000 0.034626 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029071 0.00000