HEADER TRANSFERASE 01-DEC-03 1VIS TITLE CRYSTAL STRUCTURE OF MEVALONATE KINASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: MEVALONATE KINASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MK; COMPND 5 EC: 2.7.1.36; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOCALDOCOCCUS JANNASCHII; SOURCE 3 ORGANISM_TAXID: 2190; SOURCE 4 GENE: MVK, MJ1087; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS STRUCTURAL GENOMICS, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR STRUCTURAL GENOMIX REVDAT 5 27-DEC-23 1VIS 1 REMARK REVDAT 4 04-OCT-17 1VIS 1 REMARK REVDAT 3 24-FEB-09 1VIS 1 VERSN REVDAT 2 30-AUG-05 1VIS 1 JRNL REVDAT 1 30-DEC-03 1VIS 0 JRNL AUTH J.BADGER,J.M.SAUDER,J.M.ADAMS,S.ANTONYSAMY,K.BAIN, JRNL AUTH 2 M.G.BERGSEID,S.G.BUCHANAN,M.D.BUCHANAN,Y.BATIYENKO, JRNL AUTH 3 J.A.CHRISTOPHER,S.EMTAGE,A.EROSHKINA,I.FEIL,E.B.FURLONG, JRNL AUTH 4 K.S.GAJIWALA,X.GAO,D.HE,J.HENDLE,A.HUBER,K.HODA,P.KEARINS, JRNL AUTH 5 C.KISSINGER,B.LAUBERT,H.A.LEWIS,J.LIN,K.LOOMIS,D.LORIMER, JRNL AUTH 6 G.LOUIE,M.MALETIC,C.D.MARSH,I.MILLER,J.MOLINARI, JRNL AUTH 7 H.J.MULLER-DIECKMANN,J.M.NEWMAN,B.W.NOLAND,B.PAGARIGAN, JRNL AUTH 8 F.PARK,T.S.PEAT,K.W.POST,S.RADOJICIC,A.RAMOS,R.ROMERO, JRNL AUTH 9 M.E.RUTTER,W.E.SANDERSON,K.D.SCHWINN,J.TRESSER,J.WINHOVEN, JRNL AUTH10 T.A.WRIGHT,L.WU,J.XU,T.J.HARRIS JRNL TITL STRUCTURAL ANALYSIS OF A SET OF PROTEINS RESULTING FROM A JRNL TITL 2 BACTERIAL GENOMICS PROJECT JRNL REF PROTEINS V. 60 787 2005 JRNL REFN ISSN 0887-3585 JRNL PMID 16021622 JRNL DOI 10.1002/PROT.20541 REMARK 2 REMARK 2 RESOLUTION. 2.69 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 4.0 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) : 2.69 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.57 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 8831 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) : 0.275 REMARK 3 FREE R VALUE : 0.337 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 450 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2482 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 43 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 62.92 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.74100 REMARK 3 B22 (A**2) : -1.65000 REMARK 3 B33 (A**2) : 0.24500 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 5.15500 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.008 ; NULL REMARK 3 ANGLE DISTANCE (A) : 1.529 ; 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) : 0.005 ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.104 ; 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) : 1.287 ; 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) : 2.985 ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : 5.054 ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : 5.328 ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : 7.241 ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1VIS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-DEC-03. REMARK 100 THE DEPOSITION ID IS D_1000001905. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 32-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.9794 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM, TRUNCATE REMARK 200 DATA SCALING SOFTWARE : SCALA, CCP4 (SCALA, TRUNCATE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11993 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 36.570 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 200 DATA REDUNDANCY : 2.700 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.34000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT 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 (%): 44.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 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 22.25300 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 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 MET A -1 REMARK 465 GLY A 314 REMARK 465 GLY A 315 REMARK 465 SER A 316 REMARK 465 HIS A 317 REMARK 465 HIS A 318 REMARK 465 HIS A 319 REMARK 465 HIS A 320 REMARK 465 HIS A 321 REMARK 465 HIS A 322 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 GLU A 14 -70.08 -13.29 REMARK 500 GLN A 40 52.40 78.43 REMARK 500 ASP A 42 37.28 85.76 REMARK 500 LYS A 162 172.72 54.25 REMARK 500 ASN A 169 -92.23 60.24 REMARK 500 ASN A 170 27.12 -153.89 REMARK 500 LYS A 176 -136.78 -112.39 REMARK 500 LYS A 209 44.85 -82.04 REMARK 500 ASN A 251 47.05 32.50 REMARK 500 LYS A 300 30.62 -74.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DIO A 323 DBREF 1VIS A 2 312 UNP Q58487 KIME_METJA 2 312 SEQADV 1VIS MET A -1 UNP Q58487 CLONING ARTIFACT SEQADV 1VIS SER A 0 UNP Q58487 CLONING ARTIFACT SEQADV 1VIS LEU A 1 UNP Q58487 CLONING ARTIFACT SEQADV 1VIS GLU A 313 UNP Q58487 CLONING ARTIFACT SEQADV 1VIS GLY A 314 UNP Q58487 CLONING ARTIFACT SEQADV 1VIS GLY A 315 UNP Q58487 CLONING ARTIFACT SEQADV 1VIS SER A 316 UNP Q58487 CLONING ARTIFACT SEQADV 1VIS HIS A 317 UNP Q58487 CLONING ARTIFACT SEQADV 1VIS HIS A 318 UNP Q58487 CLONING ARTIFACT SEQADV 1VIS HIS A 319 UNP Q58487 CLONING ARTIFACT SEQADV 1VIS HIS A 320 UNP Q58487 CLONING ARTIFACT SEQADV 1VIS HIS A 321 UNP Q58487 CLONING ARTIFACT SEQADV 1VIS HIS A 322 UNP Q58487 CLONING ARTIFACT SEQRES 1 A 324 MET SER LEU ILE ILE GLU THR PRO SER LYS VAL ILE LEU SEQRES 2 A 324 PHE GLY GLU HIS ALA VAL VAL TYR GLY TYR ARG ALA ILE SEQRES 3 A 324 SER MET ALA ILE ASP LEU THR SER THR ILE GLU ILE LYS SEQRES 4 A 324 GLU THR GLN GLU ASP GLU ILE ILE LEU ASN LEU ASN ASP SEQRES 5 A 324 LEU ASN LYS SER LEU GLY LEU ASN LEU ASN GLU ILE LYS SEQRES 6 A 324 ASN ILE ASN PRO ASN ASN PHE GLY ASP PHE LYS TYR CYS SEQRES 7 A 324 LEU CYS ALA ILE LYS ASN THR LEU ASP TYR LEU ASN ILE SEQRES 8 A 324 GLU PRO LYS THR GLY PHE LYS ILE ASN ILE SER SER LYS SEQRES 9 A 324 ILE PRO ILE SER CYS GLY LEU GLY SER SER ALA SER ILE SEQRES 10 A 324 THR ILE GLY THR ILE LYS ALA VAL SER GLY PHE TYR ASN SEQRES 11 A 324 LYS GLU LEU LYS ASP ASP GLU ILE ALA LYS LEU GLY TYR SEQRES 12 A 324 MET VAL GLU LYS GLU ILE GLN GLY LYS ALA SER ILE THR SEQRES 13 A 324 ASP THR SER THR ILE THR TYR LYS GLY ILE LEU GLU ILE SEQRES 14 A 324 LYS ASN ASN LYS PHE ARG LYS ILE LYS GLY GLU PHE GLU SEQRES 15 A 324 GLU PHE LEU LYS ASN CYS LYS PHE LEU ILE VAL TYR ALA SEQRES 16 A 324 GLU LYS ARG LYS LYS LYS THR ALA GLU LEU VAL ASN GLU SEQRES 17 A 324 VAL ALA LYS ILE GLU ASN LYS ASP GLU ILE PHE LYS GLU SEQRES 18 A 324 ILE ASP LYS VAL ILE ASP GLU ALA LEU LYS ILE LYS ASN SEQRES 19 A 324 LYS GLU ASP PHE GLY LYS LEU MET THR LYS ASN HIS GLU SEQRES 20 A 324 LEU LEU LYS LYS LEU ASN ILE SER THR PRO LYS LEU ASP SEQRES 21 A 324 ARG ILE VAL ASP ILE GLY ASN ARG PHE GLY PHE GLY ALA SEQRES 22 A 324 LYS LEU THR GLY ALA GLY GLY GLY GLY CYS VAL ILE ILE SEQRES 23 A 324 LEU VAL ASN GLU GLU LYS GLU LYS GLU LEU LEU LYS GLU SEQRES 24 A 324 LEU ASN LYS GLU ASP VAL ARG ILE PHE ASN CYS ARG MET SEQRES 25 A 324 MET ASN GLU GLY GLY SER HIS HIS HIS HIS HIS HIS HET DIO A 323 6 HETNAM DIO 1,4-DIETHYLENE DIOXIDE FORMUL 2 DIO C4 H8 O2 FORMUL 3 HOH *43(H2 O) HELIX 1 1 HIS A 15 GLY A 20 5 6 HELIX 2 2 GLU A 61 ILE A 65 5 5 HELIX 3 3 ASN A 66 ASP A 72 5 7 HELIX 4 4 PHE A 73 ASN A 88 1 16 HELIX 5 5 GLY A 110 TYR A 127 1 18 HELIX 6 6 LYS A 132 GLY A 149 1 18 HELIX 7 7 ILE A 153 LYS A 162 1 10 HELIX 8 8 LYS A 176 ASN A 185 1 10 HELIX 9 9 LYS A 199 LYS A 209 1 11 HELIX 10 10 ASN A 212 LYS A 229 1 18 HELIX 11 11 ASN A 232 LYS A 248 1 17 HELIX 12 12 LYS A 249 ASN A 251 5 3 HELIX 13 13 THR A 254 GLY A 268 1 15 HELIX 14 14 LYS A 290 LYS A 300 1 11 SHEET 1 A 5 LEU A 1 PHE A 12 0 SHEET 2 A 5 ARG A 22 GLU A 38 -1 O ILE A 34 N ILE A 3 SHEET 3 A 5 PHE A 95 SER A 101 -1 O LYS A 96 N LYS A 37 SHEET 4 A 5 GLU A 43 LEU A 48 1 N ASN A 47 O ILE A 99 SHEET 5 A 5 LYS A 53 ASN A 58 -1 O LEU A 57 N ILE A 44 SHEET 1 B 4 LEU A 1 PHE A 12 0 SHEET 2 B 4 ARG A 22 GLU A 38 -1 O ILE A 34 N ILE A 3 SHEET 3 B 4 ILE A 164 LYS A 168 -1 O ILE A 167 N ALA A 23 SHEET 4 B 4 LYS A 171 LYS A 174 -1 O LYS A 171 N LYS A 168 SHEET 1 C 4 GLY A 270 THR A 274 0 SHEET 2 C 4 GLY A 280 LEU A 285 -1 O ILE A 283 N LYS A 272 SHEET 3 C 4 PHE A 188 GLU A 194 -1 N GLU A 194 O GLY A 280 SHEET 4 C 4 ARG A 304 CYS A 308 -1 O ARG A 304 N TYR A 192 SITE 1 AC1 5 SER A 106 GLY A 110 SER A 111 SER A 112 SITE 2 AC1 5 HOH A 363 CRYST1 56.347 44.506 65.880 90.00 103.09 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 0.017747 0.000000 0.004127 0.00000 SCALE2 0.000000 0.022469 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015584 0.00000