PDB Short entry for 3V85 HEADER HYDROLASE 22-DEC-11 3V85 TITLE 1.9 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF THE PROTEIN Q9SIY3 FROM TITLE 2 ARABIDOPSIS THALIANA COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTH-LIKE PHOSPHATASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TRIPHOSPHATE TUNNEL METALLOENZYME-LIKE PHOSPHATASE; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: MOUSE-EAR CRESS,THALE-CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: AT2G11890; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28 KEYWDS CYTH DOMAIN, PHOSPHATASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR C.GARCIA,G.FUCILE,P.PETIT,D.CHRISTENDAT REVDAT 2 28-FEB-24 3V85 1 REMARK REVDAT 1 07-NOV-12 3V85 0 JRNL AUTH C.GARCIA,G.FUCILE,W.MOEDER,D.CHRISTENDAT,K.YOSHIOKA JRNL TITL A YEAST-LIKE MRNA TRIPHOSPHATASE FROM ARABIDOPSIS THALIANA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: DEV_237) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.73 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.020 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 16545 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 840 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 19.7299 - 3.4477 0.99 2759 160 0.1568 0.1937 REMARK 3 2 3.4477 - 2.7389 0.98 2697 127 0.1708 0.2430 REMARK 3 3 2.7389 - 2.3933 0.97 2645 129 0.1778 0.2817 REMARK 3 4 2.3933 - 2.1748 0.97 2622 148 0.1709 0.2067 REMARK 3 5 2.1748 - 2.0191 0.95 2562 141 0.1795 0.2354 REMARK 3 6 2.0191 - 1.9001 0.90 2420 135 0.2281 0.2958 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.38 REMARK 3 B_SOL : 40.66 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.640 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 8.22080 REMARK 3 B22 (A**2) : -3.16870 REMARK 3 B33 (A**2) : -5.05200 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.37980 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 1710 REMARK 3 ANGLE : 1.035 2305 REMARK 3 CHIRALITY : 0.071 253 REMARK 3 PLANARITY : 0.004 298 REMARK 3 DIHEDRAL : 16.627 651 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 1:94) REMARK 3 ORIGIN FOR THE GROUP (A): 32.7552 14.8921 17.5175 REMARK 3 T TENSOR REMARK 3 T11: 0.1012 T22: 0.1050 REMARK 3 T33: 0.1112 T12: 0.0128 REMARK 3 T13: -0.0039 T23: -0.0056 REMARK 3 L TENSOR REMARK 3 L11: 0.1786 L22: 0.4279 REMARK 3 L33: 0.9787 L12: -0.0679 REMARK 3 L13: -0.3802 L23: 0.3241 REMARK 3 S TENSOR REMARK 3 S11: -0.0342 S12: 0.0141 S13: -0.0198 REMARK 3 S21: -0.0842 S22: 0.0021 S23: 0.0643 REMARK 3 S31: 0.0429 S32: -0.1011 S33: 0.0344 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 95:133) REMARK 3 ORIGIN FOR THE GROUP (A): 31.5778 21.5132 35.3808 REMARK 3 T TENSOR REMARK 3 T11: 0.1567 T22: 0.1090 REMARK 3 T33: 0.1078 T12: 0.0098 REMARK 3 T13: 0.0022 T23: -0.0034 REMARK 3 L TENSOR REMARK 3 L11: 0.8542 L22: 0.9246 REMARK 3 L33: 1.0874 L12: 0.2158 REMARK 3 L13: -0.5097 L23: 0.2516 REMARK 3 S TENSOR REMARK 3 S11: 0.0094 S12: -0.1810 S13: 0.0299 REMARK 3 S21: 0.4625 S22: -0.0808 S23: 0.0763 REMARK 3 S31: -0.1506 S32: 0.0717 S33: 0.0437 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 134:172) REMARK 3 ORIGIN FOR THE GROUP (A): 33.5049 9.5915 13.3146 REMARK 3 T TENSOR REMARK 3 T11: 0.1144 T22: 0.1167 REMARK 3 T33: 0.1341 T12: -0.0252 REMARK 3 T13: 0.0097 T23: 0.0012 REMARK 3 L TENSOR REMARK 3 L11: 0.1994 L22: 0.6669 REMARK 3 L33: 0.3716 L12: -0.1952 REMARK 3 L13: 0.0302 L23: 0.3913 REMARK 3 S TENSOR REMARK 3 S11: -0.0414 S12: 0.0895 S13: -0.0201 REMARK 3 S21: -0.0427 S22: -0.0659 S23: 0.1127 REMARK 3 S31: 0.0851 S32: -0.0285 S33: 0.0909 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 173:210) REMARK 3 ORIGIN FOR THE GROUP (A): 28.6324 13.0769 4.6659 REMARK 3 T TENSOR REMARK 3 T11: 0.1573 T22: 0.2393 REMARK 3 T33: 0.1105 T12: 0.0194 REMARK 3 T13: -0.0313 T23: -0.0326 REMARK 3 L TENSOR REMARK 3 L11: 0.9840 L22: 1.1176 REMARK 3 L33: 0.2074 L12: 0.0966 REMARK 3 L13: 0.2579 L23: 0.4193 REMARK 3 S TENSOR REMARK 3 S11: 0.0815 S12: 0.2331 S13: 0.0870 REMARK 3 S21: -0.3099 S22: -0.0660 S23: 0.2118 REMARK 3 S31: -0.0742 S32: -0.4008 S33: 0.0385 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3V85 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JAN-12. REMARK 100 THE DEPOSITION ID IS D_1000069715. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUN-10; 13-AUG-09 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 5.4 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : CHESS; APS REMARK 200 BEAMLINE : F2; 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97860; 0.97948 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210; ADSC QUANTUM REMARK 200 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17111 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 19.730 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.11700 REMARK 200 R SYM (I) : 0.09900 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.69700 REMARK 200 R SYM FOR SHELL (I) : 0.58500 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD 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 (%): 45.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M NACITRATE, 0.25M NH4(OAC), 30% REMARK 280 PEG4000, PH 5.4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 298.0K 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 16.97600 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 ALA A 59 REMARK 465 ALA A 60 REMARK 465 VAL A 61 REMARK 465 SER A 62 REMARK 465 ALA A 63 REMARK 465 ALA A 64 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 174 71.82 -119.57 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 CIT A 301 DBREF 3V85 A 1 210 UNP Q9SIY3 Q9SIY3_ARATH 1 210 SEQRES 1 A 210 MET GLU VAL GLU VAL LYS LEU ARG LEU LEU THR ALA ALA SEQRES 2 A 210 ALA HIS LEU ARG LEU THR THR LEU LEU THR PRO TYR HIS SEQRES 3 A 210 LEU LYS THR LEU HIS GLN ARG ASN THR PHE PHE ASP THR SEQRES 4 A 210 PRO LYS ASN ASP LEU SER LEU ARG ARG ALA VAL LEU ARG SEQRES 5 A 210 LEU ARG PHE LEU GLN ASN ALA ALA VAL SER ALA ALA SER SEQRES 6 A 210 PRO SER PRO PRO ARG CYS ILE VAL SER LEU LYS ALA LYS SEQRES 7 A 210 PRO THR LEU ALA ASN GLY ILE SER ARG VAL GLU GLU ASP SEQRES 8 A 210 GLU GLU GLU ILE GLU TYR TRP ILE GLY LYS GLU CYS VAL SEQRES 9 A 210 GLU SER PRO ALA LYS LEU SER ASP ILE GLY SER ARG VAL SEQRES 10 A 210 LEU LYS ARG VAL LYS GLU GLU TYR GLY PHE ASN ASP PHE SEQRES 11 A 210 LEU GLY PHE VAL CYS LEU GLY GLY PHE GLU ASN VAL ARG SEQRES 12 A 210 ASN VAL TYR GLU TRP ARG GLY VAL LYS LEU GLU VAL ASP SEQRES 13 A 210 GLU THR LYS TYR ASP PHE GLY ASN CYS TYR GLU ILE GLU SEQRES 14 A 210 CYS GLU THR GLU GLU PRO GLU ARG VAL LYS THR MET ILE SEQRES 15 A 210 GLU GLU PHE LEU THR GLU GLU LYS ILE GLU PHE SER ASN SEQRES 16 A 210 SER ASP MET THR LYS PHE ALA VAL PHE ARG SER GLY LYS SEQRES 17 A 210 LEU PRO HET CIT A 301 13 HETNAM CIT CITRIC ACID FORMUL 2 CIT C6 H8 O7 FORMUL 3 HOH *132(H2 O) HELIX 1 1 THR A 11 LEU A 22 1 12 HELIX 2 2 ASN A 42 ARG A 47 1 6 HELIX 3 3 GLU A 96 SER A 106 1 11 HELIX 4 4 PRO A 107 ILE A 113 5 7 HELIX 5 5 SER A 115 GLY A 126 1 12 HELIX 6 6 GLU A 174 GLU A 189 1 16 HELIX 7 7 THR A 199 GLY A 207 1 9 SHEET 1 A10 PHE A 193 ASN A 195 0 SHEET 2 A10 GLU A 2 LEU A 9 -1 N ARG A 8 O SER A 194 SHEET 3 A10 GLY A 163 GLU A 171 -1 O CYS A 170 N VAL A 5 SHEET 4 A10 VAL A 151 TYR A 160 -1 N THR A 158 O CYS A 165 SHEET 5 A10 VAL A 134 TRP A 148 -1 N ASN A 144 O VAL A 155 SHEET 6 A10 HIS A 26 ASP A 38 -1 N LEU A 27 O VAL A 145 SHEET 7 A10 ALA A 49 GLN A 57 -1 O GLN A 57 N HIS A 31 SHEET 8 A10 ARG A 70 ALA A 82 -1 O ILE A 72 N ARG A 54 SHEET 9 A10 ILE A 85 ILE A 95 -1 O GLU A 93 N VAL A 73 SHEET 10 A10 GLU A 2 LEU A 9 -1 N GLU A 4 O SER A 86 CISPEP 1 SER A 65 PRO A 66 0 -1.92 SITE 1 AC1 10 LYS A 6 ARG A 52 ARG A 54 LYS A 76 SITE 2 AC1 10 ARG A 143 GLU A 169 THR A 199 LYS A 200 SITE 3 AC1 10 HOH A 410 HOH A 454 CRYST1 44.776 33.952 71.596 90.00 95.23 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 0.022333 0.000000 0.002046 0.00000 SCALE2 0.000000 0.029453 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014026 0.00000