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 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 (PHENIX.REFINE: DEV_988) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT 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) : 2.11 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 RCSB ID CODE IS RCSB074698. 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 : AREA DETECTOR 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 : 12.700 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 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 MASTER 277 0 3 7 7 0 5 6 0 0 0 16 END