HEADER TRANSFERASE 09-JUL-01 1JJV TITLE DEPHOSPHO-COA KINASE IN COMPLEX WITH ATP COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEPHOSPHO-COA KINASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DEPHOSPHOCOENZYME A KINASE; COMPND 5 EC: 2.7.1.24; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HAEMOPHILUS INFLUENZAE; SOURCE 3 ORGANISM_TAXID: 727; SOURCE 4 GENE: YACE; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS P-LOOP NUCLEOTIDE-BINDING FOLD, STRUCTURE 2 FUNCTION PROJECT, S2F, KEYWDS 2 STRUCTURAL GENOMICS, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR G.OBMOLOVA,A.TEPLYAKOV,N.BONANDER,E.EISENSTEIN,A.J.HOWARD, AUTHOR 2 G.L.GILLILAND,STRUCTURE 2 FUNCTION PROJECT (S2F) REVDAT 3 07-FEB-24 1JJV 1 REMARK LINK REVDAT 2 24-FEB-09 1JJV 1 VERSN REVDAT 1 01-MAY-02 1JJV 0 JRNL AUTH G.OBMOLOVA,A.TEPLYAKOV,N.BONANDER,E.EISENSTEIN,A.J.HOWARD, JRNL AUTH 2 G.L.GILLILAND JRNL TITL CRYSTAL STRUCTURE OF DEPHOSPHO-COENZYME A KINASE FROM JRNL TITL 2 HAEMOPHILUS INFLUENZAE. JRNL REF J.STRUCT.BIOL. V. 136 119 2001 JRNL REFN ISSN 1047-8477 JRNL PMID 11886213 JRNL DOI 10.1006/JSBI.2001.4428 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 14850 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 800 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1544 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 37 REMARK 3 SOLVENT ATOMS : 207 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.160 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.150 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.100 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.600 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.019 ; NULL REMARK 3 ANGLE DISTANCE (A) : 1.788 ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.008 ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.122 ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL 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) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 4.200 ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : 7.800 ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : 10.800; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : 13.700; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1JJV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JUL-01. REMARK 100 THE DEPOSITION ID IS D_1000013858. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUN-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9999 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15767 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 (%) : 98.0 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05700 REMARK 200 FOR THE DATA SET : 37.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.12100 REMARK 200 FOR SHELL : 7.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, PEG 400, PH 7, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 300K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 63.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.95000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 63.00000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.95000 REMARK 290 SMTRY3 4 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 LEU A 59 REMARK 465 THR A 60 REMARK 465 GLU A 61 REMARK 465 GLN A 62 REMARK 465 GLY A 63 REMARK 465 GLU A 64 REMARK 465 GLN A 143 REMARK 465 ARG A 144 REMARK 465 ASP A 145 REMARK 465 ASN A 146 REMARK 465 ASN A 147 REMARK 465 ALA A 206 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 ASP A 125 CB - CG - OD2 ANGL. DEV. = 6.4 DEGREES REMARK 500 ARG A 165 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ASP A 170 CB - CG - OD2 ANGL. DEV. = 6.6 DEGREES REMARK 500 ASP A 171 CB - CG - OD2 ANGL. DEV. = 5.6 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 GLN A 57 -28.22 -33.98 REMARK 500 ASP A 78 -4.24 -50.90 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 HG A 302 HG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 121 O REMARK 620 2 CYS A 124 O 72.6 REMARK 620 3 CYS A 124 SG 83.1 91.0 REMARK 620 4 HOH A 382 O 93.6 100.9 166.1 REMARK 620 N 1 2 3 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 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HG A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP A 300 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HI0890 RELATED DB: TARGETDB DBREF 1JJV A 1 206 UNP P44920 COAE_HAEIN 1 206 SEQRES 1 A 206 MET THR TYR ILE VAL GLY LEU THR GLY GLY ILE GLY SER SEQRES 2 A 206 GLY LYS THR THR ILE ALA ASN LEU PHE THR ASP LEU GLY SEQRES 3 A 206 VAL PRO LEU VAL ASP ALA ASP VAL VAL ALA ARG GLU VAL SEQRES 4 A 206 VAL ALA LYS ASP SER PRO LEU LEU SER LYS ILE VAL GLU SEQRES 5 A 206 HIS PHE GLY ALA GLN ILE LEU THR GLU GLN GLY GLU LEU SEQRES 6 A 206 ASN ARG ALA ALA LEU ARG GLU ARG VAL PHE ASN HIS ASP SEQRES 7 A 206 GLU ASP LYS LEU TRP LEU ASN ASN LEU LEU HIS PRO ALA SEQRES 8 A 206 ILE ARG GLU ARG MET LYS GLN LYS LEU ALA GLU GLN THR SEQRES 9 A 206 ALA PRO TYR THR LEU PHE VAL VAL PRO LEU LEU ILE GLU SEQRES 10 A 206 ASN LYS LEU THR ALA LEU CYS ASP ARG ILE LEU VAL VAL SEQRES 11 A 206 ASP VAL SER PRO GLN THR GLN LEU ALA ARG SER ALA GLN SEQRES 12 A 206 ARG ASP ASN ASN ASN PHE GLU GLN ILE GLN ARG ILE MET SEQRES 13 A 206 ASN SER GLN VAL SER GLN GLN GLU ARG LEU LYS TRP ALA SEQRES 14 A 206 ASP ASP VAL ILE ASN ASN ASP ALA GLU LEU ALA GLN ASN SEQRES 15 A 206 LEU PRO HIS LEU GLN GLN LYS VAL LEU GLU LEU HIS GLN SEQRES 16 A 206 PHE TYR LEU GLN GLN ALA GLU ASN LYS ASN ALA HET SO4 A 301 5 HET HG A 302 1 HET ATP A 300 31 HETNAM SO4 SULFATE ION HETNAM HG MERCURY (II) ION HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE FORMUL 2 SO4 O4 S 2- FORMUL 3 HG HG 2+ FORMUL 4 ATP C10 H16 N5 O13 P3 FORMUL 5 HOH *207(H2 O) HELIX 1 1 GLY A 14 ASP A 24 1 11 HELIX 2 2 ALA A 32 VAL A 39 1 8 HELIX 3 3 SER A 44 GLY A 55 1 12 HELIX 4 4 ASN A 66 ASN A 76 1 11 HELIX 5 5 HIS A 77 GLU A 102 1 26 HELIX 6 6 LEU A 120 CYS A 124 5 5 HELIX 7 7 SER A 133 ALA A 142 1 10 HELIX 8 8 ASN A 148 GLN A 159 1 12 HELIX 9 9 SER A 161 ALA A 169 1 9 HELIX 10 10 GLU A 178 LEU A 183 1 6 HELIX 11 11 ASN A 182 LYS A 204 1 23 SHEET 1 A 5 LEU A 29 ASP A 31 0 SHEET 2 A 5 TYR A 107 VAL A 111 1 O LEU A 109 N VAL A 30 SHEET 3 A 5 TYR A 3 THR A 8 1 O TYR A 3 N THR A 108 SHEET 4 A 5 ARG A 126 ASP A 131 1 O ARG A 126 N GLY A 6 SHEET 5 A 5 ASP A 171 ASN A 174 1 N ASP A 171 O ILE A 127 LINK O THR A 121 HG HG A 302 1555 1555 2.89 LINK O CYS A 124 HG HG A 302 1555 1555 2.87 LINK SG CYS A 124 HG HG A 302 1555 1555 2.30 LINK HG HG A 302 O HOH A 382 1555 1555 2.19 SITE 1 AC1 5 ARG A 93 LYS A 97 LYS A 167 HOH A 437 SITE 2 AC1 5 HOH A 502 SITE 1 AC2 5 THR A 121 CYS A 124 ARG A 126 ILE A 127 SITE 2 AC2 5 HOH A 382 SITE 1 AC3 19 ILE A 11 GLY A 12 SER A 13 GLY A 14 SITE 2 AC3 19 LYS A 15 THR A 16 THR A 17 ASN A 86 SITE 3 AC3 19 ARG A 140 ASN A 175 ALA A 177 GLU A 178 SITE 4 AC3 19 LEU A 179 HOH A 368 HOH A 373 HOH A 376 SITE 5 AC3 19 HOH A 389 HOH A 393 HOH A 423 CRYST1 126.000 45.900 41.700 90.00 97.60 90.00 C 1 2 1 4 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 0.007937 0.000000 0.001059 0.00000 SCALE2 0.000000 0.021786 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024193 0.00000