HEADER HYDROLASE 26-JAN-04 1V9M TITLE CRYSTAL STRUCTURE OF THE C SUBUNIT OF V-TYPE ATPASE FROM THERMUS TITLE 2 THERMOPHILUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: V-TYPE ATP SYNTHASE SUBUNIT C; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: V-TYPE ATPASE SUBUNIT C, VACUOLAR ATP SYNTHASE C SUBUNIT; COMPND 5 EC: 3.6.3.14; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 274; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS VOV1-ATPASE, V-TYPE ATPASE, THE C SUBUNIT, THERMUS THERMOPHILUS, KEYWDS 2 RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, STRUCTURAL KEYWDS 3 GENOMICS, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR N.NUMOTO,A.KITA,K.MIKI,RIKEN STRUCTURAL GENOMICS/PROTEOMICS AUTHOR 2 INITIATIVE (RSGI) REVDAT 6 30-OCT-24 1V9M 1 REMARK REVDAT 5 27-DEC-23 1V9M 1 REMARK REVDAT 4 13-JUL-11 1V9M 1 VERSN REVDAT 3 01-SEP-09 1V9M 1 AUTHOR REVDAT 2 24-FEB-09 1V9M 1 VERSN REVDAT 1 04-MAY-04 1V9M 0 JRNL AUTH N.NUMOTO,A.KITA,K.MIKI JRNL TITL STRUCTURE OF THE C SUBUNIT OF V-TYPE ATPASE FROM THERMUS JRNL TITL 2 THERMOPHILUS AT 1.85 A RESOLUTION. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 60 810 2004 JRNL REFN ISSN 0907-4449 JRNL PMID 15103125 JRNL DOI 10.1107/S0907444904003257 REMARK 2 REMARK 2 RESOLUTION. 1.85 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.62 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1032460.220 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.0 REMARK 3 NUMBER OF REFLECTIONS : 24543 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) : 0.202 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1282 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.97 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3793 REMARK 3 BIN R VALUE (WORKING SET) : 0.2360 REMARK 3 BIN FREE R VALUE : 0.2500 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 205 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.017 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2458 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 165 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.04000 REMARK 3 B22 (A**2) : -0.17000 REMARK 3 B33 (A**2) : 0.20000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.09000 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) : 0.13 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) : 0.24 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.12 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.000 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 19.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.770 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) : 1.340 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.000 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.330 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.600 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 48.40 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 : GOL_XPLOR_PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : GOL_XPLOR_TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1V9M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-JAN-04. REMARK 100 THE DEPOSITION ID IS D_1000006379. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-OCT-03 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL45XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793, 0.9795, 0.9781 REMARK 200 MONOCHROMATOR : DIAMOND (4 0 0) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS V REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25341 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 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 (%) : 97.1 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.92 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.33800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 300, PEG 8000, GLYCEROL, TRIS-HCL, REMARK 280 PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 41.90300 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 ALA A 2 REMARK 465 ASP A 3 REMARK 465 ASP A 4 REMARK 465 ALA A 179 REMARK 465 ALA A 180 REMARK 465 LYS A 181 REMARK 465 GLY A 182 REMARK 465 LEU A 183 REMARK 465 ASP A 184 REMARK 465 GLN A 185 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 VAL A 69 -54.88 -134.80 REMARK 500 ARG A 223 -56.14 -137.78 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 GOL A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1002 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: TTK003000375.1 RELATED DB: TARGETDB DBREF 1V9M A 1 323 UNP P74902 VATC_THET8 1 323 SEQRES 1 A 323 MET ALA ASP ASP PHE ALA TYR LEU ASN ALA ARG VAL ARG SEQRES 2 A 323 VAL ARG ARG GLY THR LEU LEU LYS GLU SER PHE PHE GLN SEQRES 3 A 323 GLU ALA LEU ASP LEU SER PHE ALA ASP PHE LEU ARG LEU SEQRES 4 A 323 LEU SER GLU THR VAL TYR GLY GLY GLU LEU ALA GLY GLN SEQRES 5 A 323 GLY LEU PRO ASP VAL ASP ARG ALA VAL LEU ARG THR GLN SEQRES 6 A 323 ALA LYS LEU VAL GLY ASP LEU PRO ARG LEU VAL THR GLY SEQRES 7 A 323 GLU ALA ARG GLU ALA VAL ARG LEU LEU LEU LEU ARG ASN SEQRES 8 A 323 ASP LEU HIS ASN LEU GLN ALA LEU LEU ARG ALA LYS ALA SEQRES 9 A 323 THR GLY ARG PRO PHE GLU GLU VAL LEU LEU LEU PRO GLY SEQRES 10 A 323 THR LEU ARG GLU GLU VAL TRP ARG GLN ALA TYR GLU ALA SEQRES 11 A 323 GLN ASP PRO ALA GLY MET ALA GLN VAL LEU ALA VAL PRO SEQRES 12 A 323 GLY HIS PRO LEU ALA ARG ALA LEU ARG ALA VAL LEU ARG SEQRES 13 A 323 GLU THR GLN ASP LEU ALA ARG VAL GLU ALA LEU LEU ALA SEQRES 14 A 323 LYS ARG PHE PHE GLU ASP VAL ALA LYS ALA ALA LYS GLY SEQRES 15 A 323 LEU ASP GLN PRO ALA LEU ARG ASP TYR LEU ALA LEU GLU SEQRES 16 A 323 VAL ASP ALA GLU ASN LEU ARG THR ALA PHE LYS LEU GLN SEQRES 17 A 323 GLY SER GLY LEU ALA PRO ASP ALA PHE PHE LEU LYS GLY SEQRES 18 A 323 GLY ARG PHE VAL ASP ARG VAL ARG PHE ALA ARG LEU MET SEQRES 19 A 323 GLU GLY ASP TYR ALA VAL LEU ASP GLU LEU SER GLY THR SEQRES 20 A 323 PRO PHE SER GLY LEU SER GLY VAL ARG ASP LEU LYS ALA SEQRES 21 A 323 LEU GLU ARG GLY LEU ARG CYS VAL LEU LEU LYS GLU ALA SEQRES 22 A 323 LYS LYS GLY VAL GLN ASP PRO LEU GLY VAL GLY LEU VAL SEQRES 23 A 323 LEU ALA TYR VAL LYS GLU ARG GLU TRP GLU ALA VAL ARG SEQRES 24 A 323 LEU ARG LEU LEU ALA ARG ARG ALA TYR PHE GLY LEU PRO SEQRES 25 A 323 ARG ALA GLN VAL GLU GLU GLU VAL VAL CYS PRO HET GOL A1001 6 HET GOL A1002 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 2(C3 H8 O3) FORMUL 4 HOH *165(H2 O) HELIX 1 1 PHE A 5 GLY A 17 1 13 HELIX 2 2 LYS A 21 LEU A 29 1 9 HELIX 3 3 SER A 32 GLU A 42 1 11 HELIX 4 4 THR A 43 LEU A 49 5 7 HELIX 5 5 GLY A 53 VAL A 69 1 17 HELIX 6 6 ASP A 71 VAL A 76 1 6 HELIX 7 7 THR A 77 THR A 105 1 29 HELIX 8 8 PRO A 108 VAL A 112 5 5 HELIX 9 9 ARG A 120 ALA A 130 1 11 HELIX 10 10 ASP A 132 VAL A 142 1 11 HELIX 11 11 HIS A 145 ARG A 156 1 12 HELIX 12 12 ASP A 160 LYS A 178 1 19 HELIX 13 13 PRO A 186 LEU A 207 1 22 HELIX 14 14 ALA A 213 PHE A 217 5 5 HELIX 15 15 ASP A 226 GLU A 235 1 10 HELIX 16 16 ASP A 237 GLU A 243 5 7 HELIX 17 17 PHE A 249 SER A 253 5 5 HELIX 18 18 ASP A 257 LYS A 274 1 18 HELIX 19 19 LYS A 275 ASP A 279 5 5 HELIX 20 20 VAL A 283 GLY A 310 1 28 HELIX 21 21 PRO A 312 VAL A 320 1 9 SSBOND 1 CYS A 267 CYS A 322 1555 1555 2.04 SITE 1 AC1 4 LEU A 37 SER A 41 LEU A 49 GLN A 52 SITE 1 AC2 1 ARG A 149 CRYST1 41.790 83.806 48.567 90.00 113.86 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 0.023929 0.000000 0.010584 0.00000 SCALE2 0.000000 0.011932 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022514 0.00000