HEADER HYDROLASE 21-FEB-13 4JCA TITLE CRYSTAL STRUCTURE OF THE APO FORM OF THE EVOLVED VARIANT OF THE TITLE 2 COMPUTATIONALLY DESIGNED SERINE HYDROLASE, OSH55.4_H1. NORTHEAST TITLE 3 STRUCTURAL GENOMICS CONSORTIUM (NESG) TARGET OR273 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE HYDROLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: OSH55.4_H1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARTIFICIAL GENE; SOURCE 3 ORGANISM_TAXID: 32630 KEYWDS STRUCTURAL GENOMICS, PSI-BIOLOGY, PROTEIN STRUCTURE INITIATIVE, KEYWDS 2 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG), HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.P.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 4 20-SEP-23 4JCA 1 REMARK REVDAT 3 08-OCT-14 4JCA 1 JRNL REVDAT 2 16-APR-14 4JCA 1 JRNL REVDAT 1 20-MAR-13 4JCA 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. 2.41 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_1316 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) : 2.41 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.40 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 6074 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.540 REMARK 3 FREE R VALUE TEST SET COUNT : 276 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 29.3981 - 3.0367 0.99 2975 127 0.1700 0.2338 REMARK 3 2 3.0367 - 2.4107 0.97 2823 149 0.2005 0.2885 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) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.900 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 40.78 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.62 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 1219 REMARK 3 ANGLE : 1.133 1649 REMARK 3 CHIRALITY : 0.073 187 REMARK 3 PLANARITY : 0.005 216 REMARK 3 DIHEDRAL : 12.971 445 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): -9.9622 1.3494 -18.8879 REMARK 3 T TENSOR REMARK 3 T11: 0.3161 T22: 0.3275 REMARK 3 T33: 0.2524 T12: -0.0157 REMARK 3 T13: -0.0022 T23: 0.0105 REMARK 3 L TENSOR REMARK 3 L11: 3.1555 L22: 4.2430 REMARK 3 L33: 2.6159 L12: 1.1086 REMARK 3 L13: 0.1280 L23: 0.4998 REMARK 3 S TENSOR REMARK 3 S11: -0.0104 S12: -0.1119 S13: 0.0282 REMARK 3 S21: 0.2160 S22: -0.0348 S23: 0.1699 REMARK 3 S31: -0.0530 S32: -0.0928 S33: 0.0252 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 4JCA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-FEB-13. REMARK 100 THE DEPOSITION ID IS D_1000077865. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-OCT-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.2 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 : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11749 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 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 (%) : 97.9 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.8000 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: 4ETJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 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: RBCL REMARK 280 0.1M, SODIUM CITRATE 0.1M, PEG 1000 40%, MICROBATCH UNDER OIL, REMARK 280 TEMPERATURE 277K, PH 4.2 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 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+1/2 REMARK 290 4555 -X+1/2,Y+1/2,-Z+1/2 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 11.82604 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.24500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 32.06644 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 11.82604 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 33.24500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 32.06644 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 -23.65208 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -64.13288 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 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: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO A 43 C - N - CA ANGL. DEV. = 10.0 DEGREES REMARK 500 LEU A 79 CA - CB - CG ANGL. DEV. = 15.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 GLN A 15 52.54 -115.33 REMARK 500 TRP A 113 13.49 56.82 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 RB A 201 RB REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 24 ND2 REMARK 620 2 HOH A 304 O 74.9 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE RB A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CIT A 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4ETJ RELATED DB: PDB REMARK 900 HOMOLOGY IS 96.8% REMARK 900 RELATED ID: NESG-OR273 RELATED DB: TARGETTRACK DBREF 4JCA A 1 167 PDB 4JCA 4JCA 1 167 SEQRES 1 A 167 MET ALA ARG ILE ARG HIS 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 SER TRP GLY ALA TRP VAL SEQRES 10 A 167 GLY GLY LEU PRO ALA GLU ALA VAL HIS ARG VAL MET GLY 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 TYR ARG SEQRES 13 A 167 ARG ALA SER LEU GLU HIS HIS HIS HIS HIS HIS HET RB A 201 1 HET CIT A 202 13 HETNAM RB RUBIDIUM ION HETNAM CIT CITRIC ACID FORMUL 2 RB RB 1+ FORMUL 3 CIT C6 H8 O7 FORMUL 4 HOH *30(H2 O) HELIX 1 1 ASP A 10 PHE A 14 5 5 HELIX 2 2 VAL A 33 GLY A 42 1 10 HELIX 3 3 PRO A 43 ARG A 51 1 9 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 ILE A 4 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 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 ILE A 74 N ASN A 21 SHEET 6 A 6 ALA A 60 GLY A 64 -1 N THR A 63 O VAL A 73 LINK ND2 ASN A 24 RB RB A 201 1555 1555 2.95 LINK RB RB A 201 O HOH A 304 1555 1555 3.13 SITE 1 AC1 1 ASN A 24 SITE 1 AC2 6 SER A 112 HIS A 146 GLY A 147 THR A 148 SITE 2 AC2 6 SER A 151 TYR A 155 CRYST1 37.870 66.490 65.690 90.00 102.50 90.00 I 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 0.026406 0.000000 0.005854 0.00000 SCALE2 0.000000 0.015040 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015593 0.00000