HEADER HYDROLASE 06-SEP-11 3TOQ TITLE ACYLPHOSPHATASE WITH MESOPHILIC SURFACE AND THERMOPHILIC CORE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ACYLPHOSPHATASE-1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ACYLPHOSPHATASE, ERYTHROCYTE ISOZYME, ACYLPHOSPHATASE, COMPND 5 ORGAN-COMMON TYPE ISOZYME, ACYLPHOSPHATE PHOSPHOHYDROLASE 1; COMPND 6 EC: 3.6.1.7; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: ACYP1, ACYPE; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ACYLPHOSPHATASE, HYDROLASE, THERMOPHILIC, AMYLOID EXPDTA X-RAY DIFFRACTION AUTHOR T.H.YU REVDAT 2 20-MAR-24 3TOQ 1 REMARK SEQADV REVDAT 1 05-SEP-12 3TOQ 0 JRNL AUTH T.H.YU,K.B.WONG JRNL TITL PROTEIN SURFACE IS THE PREFERRED REGION FOR THERMOSTABILITY JRNL TITL 2 ENGINEERING JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.4_486) 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.16 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.060 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 10048 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.080 REMARK 3 FREE R VALUE TEST SET COUNT : 1013 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 20.1617 - 3.8186 0.99 1291 142 0.1601 0.1824 REMARK 3 2 3.8186 - 3.0342 1.00 1300 149 0.1649 0.2247 REMARK 3 3 3.0342 - 2.6517 1.00 1276 143 0.1780 0.2193 REMARK 3 4 2.6517 - 2.4096 1.00 1302 149 0.1644 0.1946 REMARK 3 5 2.4096 - 2.2372 1.00 1307 141 0.1702 0.2282 REMARK 3 6 2.2372 - 2.1054 1.00 1290 145 0.1603 0.2052 REMARK 3 7 2.1054 - 2.0001 0.99 1269 144 0.1907 0.2354 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.72 REMARK 3 K_SOL : 0.41 REMARK 3 B_SOL : 42.20 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.130 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.31 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.05760 REMARK 3 B22 (A**2) : 1.05760 REMARK 3 B33 (A**2) : -2.11520 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 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 : 0.006 786 REMARK 3 ANGLE : 0.918 1060 REMARK 3 CHIRALITY : 0.064 116 REMARK 3 PLANARITY : 0.003 136 REMARK 3 DIHEDRAL : 14.034 294 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 3TOQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-SEP-11. REMARK 100 THE DEPOSITION ID IS D_1000067733. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAR-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.2 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 : MIRROR 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 : 10063 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 30.057 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 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) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.4 M SODIUM POTASSIUM, PHOSPHATE PH REMARK 280 8.2 (HAMPTON RESEARCH, INDEX SCREEN B7 CONDITION), 289 K , VAPOR REMARK 280 DIFFUSION, SITTING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 39.05000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.54553 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 21.85900 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 39.05000 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 22.54553 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 21.85900 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 39.05000 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 22.54553 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 21.85900 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 45.09106 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 43.71800 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 45.09106 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 43.71800 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 45.09106 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 43.71800 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 215 LIES ON A SPECIAL POSITION. 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 GLU A 3 REMARK 465 GLY A 4 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 ARG A 69 -66.27 -105.30 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 PO4 A 100 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: 3TNV RELATED DB: PDB DBREF 3TOQ A 1 99 UNP P07311 ACYP1_HUMAN 1 99 SEQADV 3TOQ ALA A 10 UNP P07311 VAL 10 ENGINEERED MUTATION SEQADV 3TOQ LEU A 12 UNP P07311 TYR 12 ENGINEERED MUTATION SEQADV 3TOQ MET A 27 UNP P07311 THR 27 ENGINEERED MUTATION SEQADV 3TOQ ALA A 31 UNP P07311 GLY 31 ENGINEERED MUTATION SEQADV 3TOQ VAL A 36 UNP P07311 LEU 36 ENGINEERED MUTATION SEQADV 3TOQ ALA A 50 UNP P07311 GLY 50 ENGINEERED MUTATION SEQADV 3TOQ LEU A 62 UNP P07311 MET 62 ENGINEERED MUTATION SEQADV 3TOQ ALA A 66 UNP P07311 LEU 66 ENGINEERED MUTATION SEQRES 1 A 99 MET ALA GLU GLY ASN THR LEU ILE SER ALA ASP LEU GLU SEQRES 2 A 99 ILE PHE GLY LYS VAL GLN GLY VAL PHE PHE ARG LYS HIS SEQRES 3 A 99 MET GLN ALA GLU ALA LYS LYS LEU GLY VAL VAL GLY TRP SEQRES 4 A 99 VAL GLN ASN THR ASP ARG GLY THR VAL GLN ALA GLN LEU SEQRES 5 A 99 GLN GLY PRO ILE SER LYS VAL ARG HIS LEU GLN GLU TRP SEQRES 6 A 99 ALA GLU THR ARG GLY SER PRO LYS SER HIS ILE ASP LYS SEQRES 7 A 99 ALA ASN PHE ASN ASN GLU LYS VAL ILE LEU LYS LEU ASP SEQRES 8 A 99 TYR SER ASP PHE GLN ILE VAL LYS HET PO4 A 100 5 HETNAM PO4 PHOSPHATE ION FORMUL 2 PO4 O4 P 3- FORMUL 3 HOH *115(H2 O) HELIX 1 1 PHE A 22 GLY A 35 1 14 HELIX 2 2 ILE A 56 ARG A 69 1 14 SHEET 1 A 5 HIS A 75 ILE A 87 0 SHEET 2 A 5 LEU A 7 LYS A 17 -1 N GLU A 13 O ASN A 80 SHEET 3 A 5 VAL A 48 PRO A 55 -1 O LEU A 52 N ALA A 10 SHEET 4 A 5 VAL A 37 ASN A 42 -1 N VAL A 37 O GLN A 53 SHEET 5 A 5 PHE A 95 ILE A 97 1 O GLN A 96 N GLY A 38 SITE 1 AC1 12 VAL A 18 GLN A 19 GLY A 20 VAL A 21 SITE 2 AC1 12 PHE A 22 PHE A 23 ARG A 24 ASN A 42 SITE 3 AC1 12 SER A 93 HOH A 116 HOH A 169 HOH A 203 CRYST1 78.100 78.100 65.577 90.00 90.00 120.00 H 3 9 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 0.012804 0.007392 0.000000 0.00000 SCALE2 0.000000 0.014785 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015249 0.00000