HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 26-MAR-13 4JVV TITLE CRYSTAL STRUCTURE OF THE EVOLVED VARIANT OF THE COMPUTATIONALLY TITLE 2 DESIGNED SERINE HYDROLASE, OSH55.4_H1, COVALENTLY BOUND WITH TITLE 3 DIISOPROPYL FLUOROPHOSPHATE (DFP), NORTHEAST STRUCTURAL GENOMICS TITLE 4 CONSORTIUM (NESG) TARGET OR273 COMPND MOL_ID: 1; COMPND 2 MOLECULE: EVOLVED VARIANT OF THE COMPUTATIONALLY DESIGNED SERINE COMPND 3 HYDROLASE; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_CELL_LINE: BL21(DE3) + MAGIC; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET21_NESG KEYWDS STRUCTURAL GENOMICS, PSI-BIOLOGY, PROTEIN STRUCTURE INITIATIVE, KEYWDS 2 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) TARGET OR273, KEYWDS 3 DIISOPROPYL FLUOROPHOSPHATE, OSH55.4_H1, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR A.KUZIN,S.LEW,S.RAJAGOPALAN,J.SEETHARAMAN,S.TONG,J.K.EVERETT, AUTHOR 2 T.B.ACTON,D.BAKER,G.T.MONTELIONE,L.TONG,J.F.HUNT,NORTHEAST AUTHOR 3 STRUCTURAL GENOMICS CONSORTIUM (NESG) REVDAT 5 06-DEC-23 4JVV 1 REMARK REVDAT 4 20-SEP-23 4JVV 1 LINK REVDAT 3 14-MAY-14 4JVV 1 JRNL REVDAT 2 16-APR-14 4JVV 1 JRNL REVDAT 1 24-APR-13 4JVV 0 JRNL AUTH S.RAJAGOPALAN,C.WANG,K.YU,A.P.KUZIN,F.RICHTER,S.LEW, JRNL AUTH 2 A.E.MIKLOS,M.L.MATTHEWS,J.SEETHARAMAN,M.SU,J.F.HUNT, JRNL AUTH 3 B.F.CRAVATT,D.BAKER JRNL TITL DESIGN OF ACTIVATED SERINE-CONTAINING CATALYTIC TRIADS WITH JRNL TITL 2 ATOMIC-LEVEL ACCURACY. JRNL REF NAT.CHEM.BIOL. V. 10 386 2014 JRNL REFN ISSN 1552-4450 JRNL PMID 24705591 JRNL DOI 10.1038/NCHEMBIO.1498 REMARK 2 REMARK 2 RESOLUTION. 2.29 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.2_1296 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) : 2.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.58 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.440 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 3 NUMBER OF REFLECTIONS : 7594 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.870 REMARK 3 FREE R VALUE TEST SET COUNT : 370 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 26.5820 - 3.2980 0.97 2479 128 0.1770 0.1890 REMARK 3 2 3.2980 - 2.6190 1.00 2519 128 0.2050 0.3070 REMARK 3 3 2.6190 - 2.2880 0.89 2226 114 0.2140 0.3090 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.360 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.390 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.09 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.04 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.007 1203 REMARK 3 ANGLE : 1.193 1629 REMARK 3 CHIRALITY : 0.080 185 REMARK 3 PLANARITY : 0.005 211 REMARK 3 DIHEDRAL : 14.110 451 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 12.1245 -1.0919 15.5821 REMARK 3 T TENSOR REMARK 3 T11: 0.1914 T22: 0.2175 REMARK 3 T33: 0.1488 T12: 0.0067 REMARK 3 T13: 0.0096 T23: 0.0198 REMARK 3 L TENSOR REMARK 3 L11: 2.3047 L22: 5.3235 REMARK 3 L33: 0.8947 L12: 0.1142 REMARK 3 L13: 0.2660 L23: 0.8697 REMARK 3 S TENSOR REMARK 3 S11: 0.0369 S12: 0.0230 S13: -0.0918 REMARK 3 S21: -0.4521 S22: -0.0257 S23: 0.0147 REMARK 3 S31: -0.0567 S32: 0.0293 S33: 0.0065 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 4JVV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-APR-13. REMARK 100 THE DEPOSITION ID IS D_1000078569. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-NOV-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 10 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97894 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7903 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.288 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.0000 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: BALBES REMARK 200 STARTING MODEL: PDB ENTRY 4JCA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN SOLUTION: 100MM NACL, 5MM DTT, REMARK 280 0.02% NAN3, 10MM TRIS-HCL (PH 7.5) . RESERVOIR SOLUTION: NH4CL REMARK 280 0.1M, CAPS 0.1M, PEG400 40%, MICROBATCH UNDER OIL, TEMPERATURE REMARK 280 277K, PH 10 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 35.07650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.83400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.07650 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 33.83400 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 300 REMARK: MONOMER,18.7 KD,91.8% 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 MSE A 1 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 263 O HOH A 273 2.11 REMARK 500 O HOH A 230 O HOH A 264 2.14 REMARK 500 ND2 ASN A 67 O HOH A 218 2.14 REMARK 500 OD2 ASP A 138 O HOH A 233 2.18 REMARK 500 NZ LYS A 106 O HOH A 283 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: NESG-OR273 RELATED DB: TARGETTRACK DBREF 4JVV A 1 159 PDB 4JVV 4JVV 1 159 SEQRES 1 A 159 MSE ALA ARG ILE ARG HIS VAL GLN GLY ASP ILE THR GLU SEQRES 2 A 159 PHE GLN GLY ASP ALA ILE VAL ASN ALA ALA ASN ASN TYR SEQRES 3 A 159 LEU LYS LEU GLY ALA GLY VAL ALA GLY ALA ILE LEU ARG SEQRES 4 A 159 LYS GLY GLY PRO SER ILE GLN GLU GLU CYS ASP ARG ILE SEQRES 5 A 159 GLY LYS ILE ARG VAL GLY GLU ALA ALA VAL THR GLY ALA SEQRES 6 A 159 GLY ASN LEU PRO VAL ARG TYR VAL ILE HIS ALA ALA VAL SEQRES 7 A 159 LEU GLY ASP GLU PRO ALA SER LEU GLU THR VAL ARG LYS SEQRES 8 A 159 ALA THR LYS SER ALA LEU GLU LYS ALA VAL GLU LEU GLY SEQRES 9 A 159 LEU LYS THR VAL ALA PHE THR SER TRP GLY ALA TRP VAL SEQRES 10 A 159 GLY GLY LEU PRO ALA GLU ALA VAL HIS ARG VAL MSE GLY SEQRES 11 A 159 GLU GLU ILE LYS LYS ALA PRO ASP THR LEU GLU VAL THR SEQRES 12 A 159 GLY VAL HIS GLY THR GLU LYS SVY ALA GLU ALA TYR ARG SEQRES 13 A 159 ARG ALA SER MODRES 4JVV MSE A 129 MET SELENOMETHIONINE MODRES 4JVV SVY A 151 SER HET MSE A 129 8 HET SVY A 151 16 HETNAM MSE SELENOMETHIONINE HETNAM SVY O-[BIS(1-METHYLETHOXY)PHOSPHORYL]-L-SERINE FORMUL 1 MSE C5 H11 N O2 SE FORMUL 1 SVY C9 H20 N O6 P FORMUL 2 HOH *93(H2 O) HELIX 1 1 ASP A 10 PHE A 14 5 5 HELIX 2 2 ALA A 31 GLY A 42 1 12 HELIX 3 3 PRO A 43 GLY A 53 1 11 HELIX 4 4 SER A 85 LEU A 103 1 19 HELIX 5 5 TRP A 113 VAL A 117 5 5 HELIX 6 6 PRO A 121 ALA A 136 1 16 HELIX 7 7 THR A 148 SER A 159 1 12 SHEET 1 A 6 ARG A 3 GLN A 8 0 SHEET 2 A 6 GLU A 141 HIS A 146 1 O GLY A 144 N ARG A 5 SHEET 3 A 6 THR A 107 PHE A 110 1 N PHE A 110 O VAL A 145 SHEET 4 A 6 GLY A 16 ASN A 24 1 N VAL A 20 O ALA A 109 SHEET 5 A 6 VAL A 70 LEU A 79 1 O ILE A 74 N ASN A 21 SHEET 6 A 6 ALA A 60 GLY A 64 -1 N ALA A 61 O HIS A 75 LINK C VAL A 128 N MSE A 129 1555 1555 1.33 LINK C MSE A 129 N GLY A 130 1555 1555 1.33 LINK C LYS A 150 N SVY A 151 1555 1555 1.33 LINK C SVY A 151 N ALA A 152 1555 1555 1.34 CRYST1 70.153 67.668 37.537 90.00 94.35 90.00 C 1 2 1 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 0.014255 0.000000 0.001084 0.00000 SCALE2 0.000000 0.014778 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026717 0.00000