HEADER DE NOVO PROTEIN, HYDROLASE 31-AUG-12 4GVW TITLE THREE-DIMENSIONAL STRUCTURE OF THE DE NOVO DESIGNED SERINE HYDROLASE TITLE 2 2BFQ_3, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) TARGET OR248 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DE NOVO DESIGNED SERINE HYDROLASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS STRUCTURAL GENOMICS, PSI-BIOLOGY, PROTEIN STRUCTURE INITIATIVE, KEYWDS 2 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG), DE NOVO PROTEIN, KEYWDS 3 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.KUZIN,S.LEW,J.SEETHARAMAN,S.RAJAGOPALAN,J.K.EVERETT,T.B.ACTON, AUTHOR 2 G.T.MONTELIONE,L.TONG,J.F.HUNT,NORTHEAST STRUCTURAL GENOMICS AUTHOR 3 CONSORTIUM (NESG) REVDAT 2 13-SEP-23 4GVW 1 REMARK REVDAT 1 12-SEP-12 4GVW 0 JRNL AUTH A.KUZIN,S.LEW,J.SEETHARAMAN,S.RAJAGOPALAN,J.K.EVERETT, JRNL AUTH 2 T.B.ACTON,G.T.MONTELIONE,L.TONG,J.F.HUNT JRNL TITL NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET OR248 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.11 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) : 2.11 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.43 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 10795 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.820 REMARK 3 FREE R VALUE TEST SET COUNT : 520 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 41.4350 - 3.3540 1.00 2709 132 0.1610 0.2120 REMARK 3 2 3.3540 - 2.6620 1.00 2602 135 0.1710 0.2550 REMARK 3 3 2.6620 - 2.3260 1.00 2573 130 0.1840 0.2540 REMARK 3 4 2.3260 - 2.1130 0.93 2391 123 0.1970 0.2820 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.86 REMARK 3 K_SOL : 0.38 REMARK 3 B_SOL : 36.84 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.420 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.39000 REMARK 3 B22 (A**2) : -3.21200 REMARK 3 B33 (A**2) : 7.60300 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 : 0.008 1517 REMARK 3 ANGLE : 1.003 2044 REMARK 3 CHIRALITY : 0.073 225 REMARK 3 PLANARITY : 0.005 262 REMARK 3 DIHEDRAL : 15.144 564 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): -12.6994 -15.0508 -16.0012 REMARK 3 T TENSOR REMARK 3 T11: 0.1356 T22: 0.1769 REMARK 3 T33: 0.1887 T12: 0.0064 REMARK 3 T13: 0.0041 T23: -0.0398 REMARK 3 L TENSOR REMARK 3 L11: 2.3216 L22: 2.7582 REMARK 3 L33: 2.7186 L12: -0.0560 REMARK 3 L13: -0.0637 L23: -0.8577 REMARK 3 S TENSOR REMARK 3 S11: -0.0635 S12: -0.3642 S13: 0.1322 REMARK 3 S21: 0.3806 S22: 0.0271 S23: -0.0096 REMARK 3 S31: -0.1355 S32: -0.1266 S33: 0.0366 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 4GVW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-SEP-12. REMARK 100 THE DEPOSITION ID IS D_1000074698. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-JUN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4C 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 : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10802 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 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 (%) : 95.8 REMARK 200 DATA REDUNDANCY : 12.70 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 37.0000 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: BALBES REMARK 200 SOFTWARE USED: BALBES REMARK 200 STARTING MODEL: 2BFR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 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 REMARK 280 AMMONIUM SULFATE, 0.1M MES, 40% PEG 8000, MICROBATCH UNDER OIL, REMARK 280 PH 6.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 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 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 27.82200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 31.02600 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 53.53350 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 27.82200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 31.02600 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 53.53350 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 27.82200 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 31.02600 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 53.53350 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 27.82200 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 31.02600 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 53.53350 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: BIOLOGICAL UNIT IS THE SAME AS ASYM. 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 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 GLU A 193 REMARK 465 HIS A 194 REMARK 465 HIS A 195 REMARK 465 HIS A 196 REMARK 465 HIS A 197 REMARK 465 HIS A 198 REMARK 465 HIS A 199 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 MET A 86 -113.87 53.81 REMARK 500 SER A 141 -0.11 66.88 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 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MES A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY A 203 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2BFR RELATED DB: PDB REMARK 900 HOMOLOGY ID 96.9% REMARK 900 RELATED ID: NESG-OR248 RELATED DB: TARGETTRACK DBREF 4GVW A 1 199 PDB 4GVW 4GVW 1 199 SEQRES 1 A 199 MET GLU VAL LEU PHE GLU ALA LYS VAL GLY ASP ILE THR SEQRES 2 A 199 LEU LYS LEU ALA GLN GLY ASP ILE THR GLN TYR PRO ALA SEQRES 3 A 199 LYS ALA ILE VAL ASN ALA ALA ASN LYS ARG LEU GLU HIS SEQRES 4 A 199 GLY GLY GLY VAL ALA TYR ALA ILE ALA LYS ALA CYS ALA SEQRES 5 A 199 GLY ASP ALA GLY LEU TYR THR GLU ILE SER LYS LYS ALA SEQRES 6 A 199 MET ARG GLU GLN PHE GLY ARG ASP TYR ILE ASP HIS GLY SEQRES 7 A 199 GLU VAL VAL VAL THR PRO ALA MET ASN LEU GLU GLU ARG SEQRES 8 A 199 GLY ILE LYS TYR VAL PHE HIS THR VAL GLY PRO ILE CYS SEQRES 9 A 199 SER GLY MET TRP SER GLU GLU LEU LYS GLU LYS LEU TYR SEQRES 10 A 199 LYS ALA PHE LEU GLY PRO LEU GLU LYS ALA GLU GLU MET SEQRES 11 A 199 GLY VAL GLU SER ILE ALA PHE PRO ALA VAL SER ALA GLY SEQRES 12 A 199 ILE TYR GLY CYS ASP ALA GLU LYS VAL VAL GLU THR SER SEQRES 13 A 199 LEU GLU ALA VAL LYS ASN PHE LYS GLY SER ALA VAL LYS SEQRES 14 A 199 GLU VAL ALA GLU VAL HIS GLY ALA ARG LYS SER ALA GLU SEQRES 15 A 199 VAL ALA LEU LYS VAL PHE GLU ARG SER LEU GLU HIS HIS SEQRES 16 A 199 HIS HIS HIS HIS HET PO4 A 201 5 HET MES A 202 12 HET ACY A 203 4 HETNAM PO4 PHOSPHATE ION HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID HETNAM ACY ACETIC ACID FORMUL 2 PO4 O4 P 3- FORMUL 3 MES C6 H13 N O4 S FORMUL 4 ACY C2 H4 O2 FORMUL 5 HOH *75(H2 O) HELIX 1 1 ASP A 20 TYR A 24 5 5 HELIX 2 2 GLY A 41 GLY A 53 1 13 HELIX 3 3 ASP A 54 GLY A 71 1 18 HELIX 4 4 MET A 86 GLY A 92 5 7 HELIX 5 5 SER A 109 GLY A 131 1 23 HELIX 6 6 ASP A 148 PHE A 163 1 16 HELIX 7 7 ALA A 177 LEU A 192 1 16 SHEET 1 A 7 GLU A 2 VAL A 9 0 SHEET 2 A 7 ILE A 12 GLN A 18 -1 O ILE A 12 N VAL A 9 SHEET 3 A 7 GLU A 170 HIS A 175 1 O GLU A 173 N ALA A 17 SHEET 4 A 7 SER A 134 PHE A 137 1 N PHE A 137 O ALA A 172 SHEET 5 A 7 ALA A 28 ALA A 33 1 N VAL A 30 O ALA A 136 SHEET 6 A 7 TYR A 95 VAL A 100 1 O THR A 99 N ALA A 33 SHEET 7 A 7 VAL A 81 PRO A 84 -1 N VAL A 81 O HIS A 98 SITE 1 AC1 3 TRP A 108 GLU A 110 LYS A 151 SITE 1 AC2 11 ALA A 32 ASN A 34 SER A 141 ALA A 142 SITE 2 AC2 11 GLY A 143 ILE A 144 TYR A 145 HOH A 307 SITE 3 AC2 11 HOH A 309 HOH A 317 HOH A 361 SITE 1 AC3 3 LYS A 35 ASP A 76 HIS A 77 CRYST1 55.644 62.052 107.067 90.00 90.00 90.00 I 2 2 2 8 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 0.017971 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016116 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009340 0.00000