HEADER DE NOVO PROTEIN, HYDROLASE 23-APR-12 4ESS TITLE CRYSTAL STRUCTURE OF E6D/L155R VARIANT OF DE NOVO DESIGNED SERINE TITLE 2 HYDROLASE OSH55, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) TITLE 3 TARGET OR187 COMPND MOL_ID: 1; COMPND 2 MOLECULE: OR187; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS STRUCTURAL GENOMICS, PSI-BIOLOGY, PROTEIN STRUCTURE INITIATIVE, KEYWDS 2 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) TARGET OR187, OSH55 KEYWDS 3 MUTANT E6D/L159R, SERINE HYDROLASE, DE NOVO PROTEIN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.KUZIN,M.SU,J.SEETHARAMAN,K.KORNHABER,G.KORNHABER,S.RAJAGOPALAN, AUTHOR 2 D.BAKER,J.K.EVERETT,T.B.ACTON,G.T.MONTELIONE,L.TONG,J.F.HUNT, AUTHOR 3 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) REVDAT 6 13-SEP-23 4ESS 1 REMARK REVDAT 5 14-MAY-14 4ESS 1 JRNL REVDAT 4 16-APR-14 4ESS 1 JRNL REVDAT 3 02-APR-14 4ESS 1 JRNL REVDAT 2 20-JUN-12 4ESS 1 AUTHOR JRNL REVDAT 1 13-JUN-12 4ESS 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. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_988 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) : 29.43 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 10464 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.780 REMARK 3 FREE R VALUE TEST SET COUNT : 500 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 29.4279 - 3.1692 1.00 2544 148 0.1922 0.2408 REMARK 3 2 3.1692 - 2.5159 1.00 2498 126 0.2131 0.2916 REMARK 3 3 2.5159 - 2.1980 1.00 2496 124 0.2049 0.3018 REMARK 3 4 2.1980 - 1.9971 0.97 2426 102 0.2010 0.2454 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 : 0.73 REMARK 3 K_SOL : 0.33 REMARK 3 B_SOL : 33.97 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.720 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) : 8.00300 REMARK 3 B22 (A**2) : 1.06730 REMARK 3 B33 (A**2) : -9.07030 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -3.06970 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 : 0.007 1188 REMARK 3 ANGLE : 1.142 1603 REMARK 3 CHIRALITY : 0.073 190 REMARK 3 PLANARITY : 0.005 209 REMARK 3 DIHEDRAL : 14.152 443 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): -13.4164 0.1439 -10.2663 REMARK 3 T TENSOR REMARK 3 T11: 0.1363 T22: 0.1604 REMARK 3 T33: 0.1369 T12: -0.0043 REMARK 3 T13: -0.0090 T23: -0.0023 REMARK 3 L TENSOR REMARK 3 L11: 1.2688 L22: 1.1646 REMARK 3 L33: 1.6452 L12: -0.5937 REMARK 3 L13: -0.0056 L23: -0.2116 REMARK 3 S TENSOR REMARK 3 S11: -0.0498 S12: -0.0690 S13: 0.0584 REMARK 3 S21: 0.1108 S22: 0.0351 S23: -0.1150 REMARK 3 S31: -0.0007 S32: 0.2820 S33: 0.0314 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 4ESS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-APR-12. REMARK 100 THE DEPOSITION ID IS D_1000072024. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-APR-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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) : 0.979 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : MIRROR 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 : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10472 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.997 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.1000 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 3V45 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 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:0.1M MES, REMARK 280 25% PEG8K, MICROBATCH UNDER OIL, TEMPERATURE 293KK, PH 6.5 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 57.34900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.03700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 57.34900 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 23.03700 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 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 295 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 84 REMARK 465 LEU A 113 REMARK 465 GLY A 114 REMARK 465 HIS A 163 REMARK 465 HIS A 164 REMARK 465 HIS A 165 REMARK 465 HIS A 166 REMARK 465 HIS A 167 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 82 -179.71 56.39 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3V45 RELATED DB: PDB REMARK 900 99.4% HOMOLOGUE REMARK 900 RELATED ID: NESG-OR187 RELATED DB: TARGETTRACK DBREF 4ESS A 1 167 PDB 4ESS 4ESS 1 167 SEQRES 1 A 167 MET ALA ARG ILE ARG ASP VAL GLN GLY ASP ILE THR GLU SEQRES 2 A 167 PHE GLN GLY ASP ALA ILE VAL ASN ALA ALA ASN ASN TYR SEQRES 3 A 167 LEU LYS LEU GLY ALA GLY VAL ALA GLY ALA ILE LEU ARG SEQRES 4 A 167 LYS GLY GLY PRO SER ILE GLN GLU GLU CYS ASP ARG ILE SEQRES 5 A 167 GLY LYS ILE ARG VAL GLY GLU ALA ALA VAL THR GLY ALA SEQRES 6 A 167 GLY ASN LEU PRO VAL ARG TYR VAL ILE HIS ALA ALA VAL SEQRES 7 A 167 LEU GLY ASP GLU PRO ALA SER LEU GLU THR VAL ARG LYS SEQRES 8 A 167 ALA THR LYS SER ALA LEU GLU LYS ALA VAL GLU LEU GLY SEQRES 9 A 167 LEU LYS THR VAL ALA PHE THR ALA LEU GLY ALA TRP VAL SEQRES 10 A 167 GLY GLY LEU PRO ALA GLU ALA VAL LEU ARG VAL MET LEU SEQRES 11 A 167 GLU GLU ILE LYS LYS ALA PRO ASP THR LEU GLU VAL THR SEQRES 12 A 167 GLY VAL HIS GLY THR GLU LYS SER ALA GLU ALA ALA ARG SEQRES 13 A 167 ARG ALA ARG LEU GLU HIS HIS HIS HIS HIS HIS FORMUL 2 HOH *95(H2 O) HELIX 1 1 ASP A 10 PHE A 14 5 5 HELIX 2 2 GLY A 32 GLY A 42 1 11 HELIX 3 3 PRO A 43 GLY A 53 1 11 HELIX 4 4 LEU A 86 LEU A 103 1 18 HELIX 5 5 PRO A 121 LYS A 135 1 15 HELIX 6 6 THR A 148 GLU A 161 1 14 SHEET 1 A 6 ARG A 3 GLN A 8 0 SHEET 2 A 6 GLU A 141 HIS A 146 1 O VAL A 142 N ARG A 3 SHEET 3 A 6 THR A 107 THR A 111 1 N VAL A 108 O THR A 143 SHEET 4 A 6 ALA A 18 ASN A 24 1 N VAL A 20 O ALA A 109 SHEET 5 A 6 TYR A 72 LEU A 79 1 O ALA A 76 N ALA A 23 SHEET 6 A 6 ALA A 60 GLY A 64 -1 N ALA A 61 O HIS A 75 CISPEP 1 GLU A 82 PRO A 83 0 -3.93 CISPEP 2 GLU A 161 HIS A 162 0 -6.59 CRYST1 114.698 46.074 30.179 90.00 102.84 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 0.008719 0.000000 0.001987 0.00000 SCALE2 0.000000 0.021704 0.000000 0.00000 SCALE3 0.000000 0.000000 0.033985 0.00000