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 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 (PHENIX.REFINE: 1.8.2_1296) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : 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 RCSB ID CODE IS RCSB078569. 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 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 MASTER 233 0 2 7 6 0 0 6 0 0 0 13 END