HEADER HYDROLASE 02-SEP-11 3TNV TITLE ACYLPHOSPHATASE WITH THERMOPHILIC SURFACE AND MESOPHILIC CORE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ACYLPHOSPHATASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ACYLPHOSPHATE PHOSPHOHYDROLASE; COMPND 5 EC: 3.6.1.7; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS HORIKOSHII; SOURCE 3 ORGANISM_TAXID: 70601; SOURCE 4 STRAIN: OT-3; SOURCE 5 GENE: ACYP, PH0305.1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ALPHA AND BETA PROTEINS, HYDROLASE, STABILITY, AMYLOID, PHOSPHATASE EXPDTA X-RAY DIFFRACTION AUTHOR T.H.YU,C.H.CHAN REVDAT 2 01-NOV-23 3TNV 1 REMARK SEQADV REVDAT 1 05-SEP-12 3TNV 0 JRNL AUTH T.H.YU,K.B.WONG JRNL TITL PROTEIN SURFACE IS A PREFERRED SITE FOR THERMOSTABILITY JRNL TITL 2 ENGINEERING JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.86 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 9907 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.149 REMARK 3 R VALUE (WORKING SET) : 0.146 REMARK 3 FREE R VALUE : 0.167 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.990 REMARK 3 FREE R VALUE TEST SET COUNT : 990 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 15.8583 - 3.0546 1.00 1300 145 0.1333 0.1403 REMARK 3 2 3.0546 - 2.4273 1.00 1286 142 0.1452 0.1707 REMARK 3 3 2.4273 - 2.1213 1.00 1266 142 0.1451 0.1521 REMARK 3 4 2.1213 - 1.9277 1.00 1259 139 0.1426 0.1821 REMARK 3 5 1.9277 - 1.7897 1.00 1275 142 0.1393 0.1737 REMARK 3 6 1.7897 - 1.6843 1.00 1265 140 0.1602 0.2141 REMARK 3 7 1.6843 - 1.6001 1.00 1266 140 0.2314 0.2533 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.40 REMARK 3 SHRINKAGE RADIUS : 0.04 REMARK 3 K_SOL : 0.47 REMARK 3 B_SOL : 73.58 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.440 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) : 0.12550 REMARK 3 B22 (A**2) : -0.64080 REMARK 3 B33 (A**2) : 0.51530 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.77030 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 : 0.006 756 REMARK 3 ANGLE : 0.950 1023 REMARK 3 CHIRALITY : 0.071 102 REMARK 3 PLANARITY : 0.004 134 REMARK 3 DIHEDRAL : 13.016 288 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 3TNV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-SEP-11. REMARK 100 THE DEPOSITION ID IS D_1000067702. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-MAY-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9923 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 15.860 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 1W2I REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M SODIUM CITRATE TRIBASIC REMARK 280 DEHYDRATE, 20% W/V PEG 3350 , PH 8.3, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 289K 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 22.21900 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 MET A 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 92 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1W2I RELATED DB: PDB REMARK 900 RELATED ID: 2VH7 RELATED DB: PDB REMARK 900 RELATED ID: 3TOQ RELATED DB: PDB DBREF 3TNV A 1 91 UNP P84142 ACYP_PYRHO 1 91 SEQADV 3TNV VAL A 6 UNP P84142 ALA 6 ENGINEERED MUTATION SEQADV 3TNV TYR A 8 UNP P84142 LEU 8 ENGINEERED MUTATION SEQADV 3TNV THR A 23 UNP P84142 MET 23 ENGINEERED MUTATION SEQADV 3TNV GLY A 27 UNP P84142 ALA 27 ENGINEERED MUTATION SEQADV 3TNV LEU A 32 UNP P84142 VAL 32 ENGINEERED MUTATION SEQADV 3TNV GLY A 46 UNP P84142 ALA 46 ENGINEERED MUTATION SEQADV 3TNV MET A 58 UNP P84142 LEU 58 ENGINEERED MUTATION SEQADV 3TNV LEU A 62 UNP P84142 ALA 62 ENGINEERED MUTATION SEQRES 1 A 91 MET ALA ILE VAL ARG VAL HIS TYR LYS ILE TYR GLY ARG SEQRES 2 A 91 VAL GLN GLY VAL GLY PHE ARG TRP SER THR GLN ARG GLU SEQRES 3 A 91 GLY ARG LYS LEU GLY LEU ASN GLY TRP VAL ARG ASN LEU SEQRES 4 A 91 PRO ASP GLY SER VAL GLU GLY VAL LEU GLU GLY ASP GLU SEQRES 5 A 91 GLU ARG VAL GLU ALA MET ILE GLY TRP LEU HIS GLN GLY SEQRES 6 A 91 PRO PRO LEU ALA ARG VAL THR ARG VAL GLU VAL LYS TRP SEQRES 7 A 91 GLU GLN PRO LYS GLY GLU LYS GLY PHE ARG ILE VAL GLY HET PO4 A 92 5 HETNAM PO4 PHOSPHATE ION FORMUL 2 PO4 O4 P 3- FORMUL 3 HOH *139(H2 O) HELIX 1 1 GLY A 18 LEU A 30 1 13 HELIX 2 2 GLU A 52 HIS A 63 1 12 SHEET 1 A 5 ARG A 70 GLU A 79 0 SHEET 2 A 5 ILE A 3 ARG A 13 -1 N LYS A 9 O GLU A 75 SHEET 3 A 5 VAL A 44 ASP A 51 -1 O VAL A 44 N ILE A 10 SHEET 4 A 5 ASN A 33 ASN A 38 -1 N ASN A 33 O GLU A 49 SHEET 5 A 5 PHE A 87 ILE A 89 1 O ARG A 88 N GLY A 34 SITE 1 AC1 6 GLY A 18 PHE A 19 ARG A 20 TRP A 21 SITE 2 AC1 6 HOH A 96 HOH A 161 CRYST1 28.087 44.438 30.813 90.00 100.99 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 0.035604 0.000000 0.006916 0.00000 SCALE2 0.000000 0.022504 0.000000 0.00000 SCALE3 0.000000 0.000000 0.033061 0.00000