HEADER LIGASE 06-APR-07 2YV1 TITLE CRYSTAL STRUCTURE OF SUCCINYL-COA SYNTHETASE ALPHA CHAIN FROM TITLE 2 METHANOCALDOCOCCUS JANNASCHII DSM 2661 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SUCCINYL-COA LIGASE [ADP-FORMING] SUBUNIT ALPHA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SUCCINYL-COA SYNTHETASE SUBUNIT ALPHA, SCS-ALPHA; COMPND 5 EC: 6.2.1.5; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOCALDOCOCCUS JANNASCHII; SOURCE 3 ORGANISM_TAXID: 243232; SOURCE 4 STRAIN: DSM 2661; SOURCE 5 GENE: SUCD; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-21A KEYWDS COA-BINDING DOMAIN, LIGASE, STRUCTURAL GENOMICS, NPPSFA, NATIONAL KEYWDS 2 PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES, RIKEN KEYWDS 3 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI EXPDTA X-RAY DIFFRACTION AUTHOR H.NIWA,S.KURAMITSU,S.YOKOYAMA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS AUTHOR 2 INITIATIVE (RSGI) REVDAT 4 25-OCT-23 2YV1 1 REMARK REVDAT 3 13-JUL-11 2YV1 1 VERSN REVDAT 2 24-FEB-09 2YV1 1 VERSN REVDAT 1 09-OCT-07 2YV1 0 JRNL AUTH H.NIWA,S.KURAMITSU,S.YOKOYAMA JRNL TITL CRYSTAL STRUCTURE OF SUCCINYL-COA SYNTHETASE ALPHA CHAIN JRNL TITL 2 FROM METHANOCALDOCOCCUS JANNASCHII DSM 2661 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.49 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1285654.870 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 31212 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1572 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.81 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4796 REMARK 3 BIN R VALUE (WORKING SET) : 0.2490 REMARK 3 BIN FREE R VALUE : 0.2960 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 225 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1967 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 271 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.56000 REMARK 3 B22 (A**2) : 0.05000 REMARK 3 B33 (A**2) : -1.62000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.12 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.14 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.960 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.270 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.980 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.220 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.310 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.33 REMARK 3 BSOL : 44.02 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2YV1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-JUN-07. REMARK 100 THE DEPOSITION ID IS D_1000027169. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-DEC-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL38B1 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 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU JUPITER 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31324 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 (%) : 98.8 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 44.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.20 REMARK 200 R MERGE FOR SHELL (I) : 0.36600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1OI7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM ACETATE, 20% PEG 3350, REMARK 280 0.2M LITHIUM SULFATE, PH5.6, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 32.94100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.97900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.52200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.97900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.94100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.52200 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 MET A 1 REMARK 465 VAL A 2 REMARK 465 LEU A 3 REMARK 465 ARG A 4 REMARK 465 ASP A 5 REMARK 465 LYS A 6 REMARK 465 SER A 242 REMARK 465 ALA A 243 REMARK 465 PRO A 244 REMARK 465 GLU A 245 REMARK 465 GLY A 246 REMARK 465 LYS A 247 REMARK 465 ARG A 248 REMARK 465 MET A 249 REMARK 465 GLY A 250 REMARK 465 HIS A 251 REMARK 465 ALA A 252 REMARK 465 GLY A 253 REMARK 465 ALA A 254 REMARK 465 ILE A 255 REMARK 465 VAL A 256 REMARK 465 GLU A 257 REMARK 465 LYS A 258 REMARK 465 GLY A 259 REMARK 465 LYS A 260 REMARK 465 LYS A 294 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 MET A 7 CG SD CE REMARK 470 LYS A 231 CG CD CE NZ 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 LEU A 9 -104.77 -104.46 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: MJA001001246.1 RELATED DB: TARGETDB DBREF 2YV1 A 1 294 UNP Q58643 SUCD_METJA 1 294 SEQRES 1 A 294 MET VAL LEU ARG ASP LYS MET ILE LEU LEU ASP GLU ASN SEQRES 2 A 294 THR LYS ALA ILE VAL GLN GLY ILE THR GLY ARG GLN GLY SEQRES 3 A 294 SER PHE HIS THR LYS LYS MET LEU GLU CYS GLY THR LYS SEQRES 4 A 294 ILE VAL GLY GLY VAL THR PRO GLY LYS GLY GLY GLN ASN SEQRES 5 A 294 VAL HIS GLY VAL PRO VAL PHE ASP THR VAL LYS GLU ALA SEQRES 6 A 294 VAL LYS GLU THR ASP ALA ASN ALA SER VAL ILE PHE VAL SEQRES 7 A 294 PRO ALA PRO PHE ALA LYS ASP ALA VAL PHE GLU ALA ILE SEQRES 8 A 294 ASP ALA GLY ILE GLU LEU ILE VAL VAL ILE THR GLU HIS SEQRES 9 A 294 ILE PRO VAL HIS ASP THR MET GLU PHE VAL ASN TYR ALA SEQRES 10 A 294 GLU ASP VAL GLY VAL LYS ILE ILE GLY PRO ASN THR PRO SEQRES 11 A 294 GLY ILE ALA SER PRO LYS VAL GLY LYS LEU GLY ILE ILE SEQRES 12 A 294 PRO MET GLU VAL LEU LYS GLU GLY SER VAL GLY MET VAL SEQRES 13 A 294 SER ARG SER GLY THR LEU THR TYR GLU ILE ALA HIS GLN SEQRES 14 A 294 ILE LYS LYS ALA GLY PHE GLY VAL SER THR CYS VAL GLY SEQRES 15 A 294 ILE GLY GLY ASP PRO ILE VAL GLY LEU ARG TYR LYS GLU SEQRES 16 A 294 VAL LEU ASP LEU PHE GLU LYS ASP ASP GLU THR GLU ALA SEQRES 17 A 294 ILE VAL MET ILE GLY GLU ILE GLY GLY GLY ALA GLU GLU SEQRES 18 A 294 GLU ALA ALA LYS PHE ILE GLU LYS MET LYS LYS PRO VAL SEQRES 19 A 294 ILE GLY TYR ILE ALA GLY GLN SER ALA PRO GLU GLY LYS SEQRES 20 A 294 ARG MET GLY HIS ALA GLY ALA ILE VAL GLU LYS GLY LYS SEQRES 21 A 294 GLY THR ALA GLU SER LYS MET LYS ALA LEU GLU GLU ALA SEQRES 22 A 294 GLY ALA TYR VAL ALA LYS ASN ILE SER ASP ILE PRO LYS SEQRES 23 A 294 LEU LEU ALA GLY ILE LEU GLY LYS FORMUL 2 HOH *271(H2 O) HELIX 1 1 GLY A 23 CYS A 36 1 14 HELIX 2 2 THR A 61 ASP A 70 1 10 HELIX 3 3 PRO A 79 ALA A 93 1 15 HELIX 4 4 PRO A 106 GLY A 121 1 16 HELIX 5 5 PRO A 144 LEU A 148 5 5 HELIX 6 6 GLY A 160 ALA A 173 1 14 HELIX 7 7 ARG A 192 LYS A 202 1 11 HELIX 8 8 GLY A 218 GLU A 228 1 11 HELIX 9 9 THR A 262 GLY A 274 1 13 HELIX 10 10 SER A 282 GLY A 293 1 12 SHEET 1 A 7 ASN A 52 VAL A 53 0 SHEET 2 A 7 VAL A 56 PHE A 59 -1 O VAL A 56 N VAL A 53 SHEET 3 A 7 ILE A 40 VAL A 44 1 N GLY A 43 O PHE A 59 SHEET 4 A 7 ALA A 16 GLN A 19 1 N VAL A 18 O VAL A 44 SHEET 5 A 7 ALA A 73 ILE A 76 1 O VAL A 75 N GLN A 19 SHEET 6 A 7 LEU A 97 VAL A 100 1 O VAL A 99 N ILE A 76 SHEET 7 A 7 LYS A 123 ILE A 125 1 O LYS A 123 N ILE A 98 SHEET 1 B 7 GLY A 138 GLY A 141 0 SHEET 2 B 7 GLY A 131 SER A 134 -1 N SER A 134 O GLY A 138 SHEET 3 B 7 VAL A 177 GLY A 182 -1 O CYS A 180 N ALA A 133 SHEET 4 B 7 VAL A 153 SER A 157 1 N MET A 155 O THR A 179 SHEET 5 B 7 ALA A 208 GLU A 214 1 O VAL A 210 N GLY A 154 SHEET 6 B 7 VAL A 234 ALA A 239 1 O ILE A 235 N ILE A 209 SHEET 7 B 7 TYR A 276 VAL A 277 1 O TYR A 276 N VAL A 234 CISPEP 1 GLY A 126 PRO A 127 0 0.73 CRYST1 65.882 65.044 65.958 90.00 90.00 90.00 P 21 21 21 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 0.015179 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015374 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015161 0.00000