HEADER HYDROLASE 19-MAR-12 4E88 TITLE CRYSTAL STRUCTURE OF DE NOVO DESIGNED CYSTEINE ESTERASE ECH13, TITLE 2 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET OR51 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DE NOVO DESIGNED CYSTEINE ESTERASE ECH13; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; 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.KUZIN,M.SU,J.SEETHARAMAN,X.XIAO,S.SAHDEV,C.CICCOSANTI,F.RICHTER, AUTHOR 2 J.K.EVERETT,T.B.ACTON,G.T.MONTELIONE,J.F.HUNT,L.TONG,NORTHEAST AUTHOR 3 STRUCTURAL GENOMICS CONSORTIUM (NESG) REVDAT 3 06-DEC-23 4E88 1 REMARK REVDAT 2 13-SEP-23 4E88 1 REMARK LINK REVDAT 1 11-APR-12 4E88 0 JRNL AUTH A.KUZIN,M.SU,J.SEETHARAMAN,X.XIAO,S.SAHDEV,C.CICCOSANTI, JRNL AUTH 2 F.RICHTER,J.K.EVERETT,T.B.ACTON,G.T.MONTELIONE,J.F.HUNT, JRNL AUTH 3 L.TONG JRNL TITL NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET OR51 JRNL REF TO BE PUBLISHED JRNL REFN 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) : 23.09 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 16344 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 828 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 23.0920 - 3.6310 1.00 2709 153 0.1600 0.1830 REMARK 3 2 3.6310 - 2.8840 1.00 2655 147 0.1870 0.2230 REMARK 3 3 2.8840 - 2.5200 1.00 2654 134 0.1860 0.2380 REMARK 3 4 2.5200 - 2.2890 1.00 2660 132 0.1700 0.2200 REMARK 3 5 2.2890 - 2.1250 0.99 2599 144 0.1810 0.2380 REMARK 3 6 2.1250 - 2.0000 0.85 2239 118 0.2500 0.3010 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.98 REMARK 3 K_SOL : 0.32 REMARK 3 B_SOL : 39.49 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.550 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.24 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.29 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.61000 REMARK 3 B22 (A**2) : 6.46800 REMARK 3 B33 (A**2) : -7.07800 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.93300 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 1677 REMARK 3 ANGLE : 1.073 2273 REMARK 3 CHIRALITY : 0.077 235 REMARK 3 PLANARITY : 0.004 300 REMARK 3 DIHEDRAL : 12.511 644 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): 10.9111 -31.2220 -10.3695 REMARK 3 T TENSOR REMARK 3 T11: 0.1149 T22: 0.1876 REMARK 3 T33: 0.1712 T12: 0.0021 REMARK 3 T13: 0.0191 T23: 0.0021 REMARK 3 L TENSOR REMARK 3 L11: 1.3812 L22: 2.0278 REMARK 3 L33: 3.7112 L12: 0.0949 REMARK 3 L13: -0.3615 L23: -1.1295 REMARK 3 S TENSOR REMARK 3 S11: 0.0231 S12: 0.1341 S13: 0.0017 REMARK 3 S21: -0.0559 S22: 0.0858 S23: 0.1192 REMARK 3 S31: -0.0043 S32: -0.4454 S33: -0.0880 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 4E88 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-MAR-12. REMARK 100 THE DEPOSITION ID IS D_1000071292. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-MAY-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16356 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 (%) : 97.3 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 30.9000 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: MIR REMARK 200 SOFTWARE USED: BALBES REMARK 200 STARTING MODEL: PDB ENTRY 3U13 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.59 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:100MM REMARK 280 NACL, 5MM DTT, 0.02% NAN3, 10MM TRIS-HCL (PH 7.5) . RESERVOIR REMARK 280 SOLUTION: 0.2M REMARK 280 NH4F, 20% PEG3350, REMARK 280 0.02% REMARK 280 NAN3, 10MM TRIS-HCL (PH 7.5) . RESERVOIR SOLUTION: 0.2M , VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 277KK 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 43.99700 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.87250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 43.99700 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 30.87250 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: DIMER,54.06 KD,98.7% 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2630 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18370 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 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 37.33127 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -46.18263 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 577 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 MSE A 1 REMARK 465 GLY A 2 REMARK 465 CYS A 198 REMARK 465 GLY A 199 REMARK 465 SER A 200 REMARK 465 LEU A 201 REMARK 465 GLU A 202 REMARK 465 HIS A 203 REMARK 465 HIS A 204 REMARK 465 HIS A 205 REMARK 465 HIS A 206 REMARK 465 HIS A 207 REMARK 465 HIS A 208 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 HIS A 103 -151.77 49.89 REMARK 500 MSE A 105 75.84 -119.86 REMARK 500 SER A 183 -178.90 -173.95 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 GOL A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3U19 RELATED DB: PDB REMARK 900 IDENTITY IS 100%. REMARK 900 RELATED ID: NESG-OX158 RELATED DB: TARGETTRACK DBREF 4E88 A 1 208 PDB 4E88 4E88 1 208 SEQRES 1 A 208 MSE GLY GLY ARG ALA LEU ARG VAL LEU VAL ASP MSE ASP SEQRES 2 A 208 GLY VAL LEU ALA ASP VAL GLU GLY GLY LEU LEU ARG LYS SEQRES 3 A 208 PHE ARG ALA ARG PHE PRO ASP GLN PRO PHE ILE ALA LEU SEQRES 4 A 208 GLU ASP ARG ARG GLY TYR LYS ALA CSO GLU GLN TYR GLY SEQRES 5 A 208 ARG LEU ARG PRO GLY LEU SER GLU LYS ALA ARG SER ILE SEQRES 6 A 208 ALA GLU SER LYS ASN PHE PHE PHE GLU LEU GLU PRO LEU SEQRES 7 A 208 PRO GLY ALA VAL GLU ALA VAL LYS GLU MSE ALA SER LEU SEQRES 8 A 208 GLN ASN THR ASP VAL PHE ILE CYS THR SER PRO HIS LYS SEQRES 9 A 208 MSE PHE LYS TYR CYS PRO TYR GLU LYS TYR ALA TRP VAL SEQRES 10 A 208 GLU LYS TYR PHE GLY PRO ASP PHE LEU GLU GLN ILE VAL SEQRES 11 A 208 LEU THR ARG ASP LYS THR VAL VAL SER ALA ASP LEU LEU SEQRES 12 A 208 ILE ASP ASP ARG PRO ASP ILE THR GLY ALA GLU PRO THR SEQRES 13 A 208 PRO SER TRP GLU HIS VAL LEU PHE THR ALA CYS HIS ASN SEQRES 14 A 208 GLN HIS LEU GLN LEU GLN PRO PRO ARG ARG ARG LEU HIS SEQRES 15 A 208 SER TRP ALA ASP ASP TRP LYS ALA ILE LEU ASP SER LYS SEQRES 16 A 208 ARG PRO CYS GLY SER LEU GLU HIS HIS HIS HIS HIS HIS MODRES 4E88 MSE A 12 MET SELENOMETHIONINE MODRES 4E88 CSO A 48 CYS S-HYDROXYCYSTEINE MODRES 4E88 MSE A 88 MET SELENOMETHIONINE MODRES 4E88 MSE A 105 MET SELENOMETHIONINE HET MSE A 12 8 HET CSO A 48 7 HET MSE A 88 8 HET MSE A 105 8 HET GOL A 301 6 HETNAM MSE SELENOMETHIONINE HETNAM CSO S-HYDROXYCYSTEINE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 1 CSO C3 H7 N O3 S FORMUL 2 GOL C3 H8 O3 FORMUL 3 HOH *183(H2 O) HELIX 1 1 ASP A 18 PHE A 31 1 14 HELIX 2 2 ALA A 38 ARG A 42 5 5 HELIX 3 3 LYS A 46 ARG A 55 1 10 HELIX 4 4 GLY A 57 SER A 68 1 12 HELIX 5 5 GLY A 80 LEU A 91 1 12 HELIX 6 6 TYR A 108 GLY A 122 1 15 HELIX 7 7 PRO A 123 GLU A 127 5 5 HELIX 8 8 ASP A 187 ARG A 196 1 10 SHEET 1 A 6 ILE A 129 LEU A 131 0 SHEET 2 A 6 THR A 94 THR A 100 1 N ILE A 98 O VAL A 130 SHEET 3 A 6 LEU A 6 VAL A 10 1 N LEU A 6 O ASP A 95 SHEET 4 A 6 LEU A 142 ASP A 145 1 O LEU A 142 N LEU A 9 SHEET 5 A 6 GLU A 160 PHE A 164 1 O VAL A 162 N LEU A 143 SHEET 6 A 6 ARG A 179 LEU A 181 1 O LEU A 181 N LEU A 163 LINK C ASP A 11 N MSE A 12 1555 1555 1.33 LINK C MSE A 12 N ASP A 13 1555 1555 1.33 LINK C ALA A 47 N CSO A 48 1555 1555 1.33 LINK C CSO A 48 N GLU A 49 1555 1555 1.33 LINK C GLU A 87 N MSE A 88 1555 1555 1.33 LINK C MSE A 88 N ALA A 89 1555 1555 1.33 LINK C LYS A 104 N MSE A 105 1555 1555 1.33 LINK C MSE A 105 N PHE A 106 1555 1555 1.32 CISPEP 1 PRO A 176 PRO A 177 0 3.93 SITE 1 AC1 6 ASP A 33 GLN A 34 PRO A 35 ARG A 55 SITE 2 AC1 6 GLY A 152 ALA A 153 CRYST1 87.994 61.745 59.384 90.00 128.95 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 0.011364 0.000000 0.009187 0.00000 SCALE2 0.000000 0.016196 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021654 0.00000