HEADER HYDROLASE 14-JUN-12 4FLE TITLE CRYSTAL STRUCTURE OF THE ESTERASE YQIA (YE3661) FROM YERSINIA TITLE 2 ENTEROCOLITICA, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET YER85 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ESTERASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: YERSINIA ENTEROCOLITICA SUBSP. ENTEROCOLITICA; SOURCE 3 ORGANISM_TAXID: 393305; SOURCE 4 STRAIN: 8081; SOURCE 5 GENE: YE3661; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)+MAGIC; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21 KEYWDS STRUCTURAL GENOMICS, PSI-BIOLOGY, NORTHEAST STRUCTURAL GENOMICS KEYWDS 2 CONSORTIUM, NESG, ALPHA-BETA PROTEIN, ROSSMANN FOLD, DISPLAYS KEYWDS 3 ESTERASE ACTIVITY TOWARD PALMITOYL-COA AND PNP-BUTYRATE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR F.FOROUHAR,S.LEW,J.SEETHARAMAN,R.SHASTRY,E.KOHAN,M.MAGLAQUI,L.MAO, AUTHOR 2 R.XIAO,T.B.ACTON,J.K.EVERETT,G.T.MONTELIONE,L.TONG,J.F.HUNT, AUTHOR 3 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM,NORTHEAST STRUCTURAL AUTHOR 4 GENOMICS CONSORTIUM (NESG) REVDAT 2 25-OCT-17 4FLE 1 REMARK REVDAT 1 08-AUG-12 4FLE 0 JRNL AUTH F.FOROUHAR,S.LEW,J.SEETHARAMAN,R.SHASTRY,E.KOHAN,M.MAGLAQUI, JRNL AUTH 2 L.MAO,R.XIAO,T.B.ACTON,J.K.EVERETT,G.T.MONTELIONE,L.TONG, JRNL AUTH 3 J.F.HUNT,NORTHEAST STRUCTURAL GENOMICS CONSORTIUM JRNL TITL CRYSTAL STRUCTURE OF THE ESTERASE YQIA (YE3661) FROM JRNL TITL 2 YERSINIA ENTEROCOLITICA, NORTHEAST STRUCTURAL GENOMICS JRNL TITL 3 CONSORTIUM TARGET YER85 (CASP TARGET) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.3 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.06 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 161453.650 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 22145 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.400 REMARK 3 FREE R VALUE TEST SET COUNT : 2078 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.23 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3109 REMARK 3 BIN R VALUE (WORKING SET) : 0.1860 REMARK 3 BIN FREE R VALUE : 0.2460 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 342 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.013 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1543 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 183 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.85000 REMARK 3 B22 (A**2) : -0.49000 REMARK 3 B33 (A**2) : 1.34000 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.22 REMARK 3 ESD FROM SIGMAA (A) : 0.07 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.28 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.15 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.720 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 54.54 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4FLE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-JUN-12. REMARK 100 THE DEPOSITION ID IS D_1000073044. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-MAR-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 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) : 0.97911 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : MIRRORS 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 : 22631 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 46.060 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : 0.05800 REMARK 200 FOR THE DATA SET : 31.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.20700 REMARK 200 R SYM FOR SHELL (I) : 0.21400 REMARK 200 FOR SHELL : 7.350 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN SOLUTION: 10 MM TRIS (PH 7.5), REMARK 280 100 MM SODIUM CHLORIDE, AND 5 MM DTT. CRYSTILLIZATION SOLUTION: REMARK 280 100 MM TRIS (PH 8), 24% PEG 20K, AND 100 MM MG(NO3)2:6H2O. , REMARK 280 MICROBATCH UNDEROIL, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 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+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 27.52800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.77150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.52800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.77150 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: MONOMER ACCORDING TO STATIC LIGHT SCATTERING. 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 MSE A 1 REMARK 465 MSE A 2 REMARK 465 HIS A 198 REMARK 465 HIS A 199 REMARK 465 HIS A 200 REMARK 465 HIS A 201 REMARK 465 HIS A 202 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 SER A 13 -165.60 -104.31 REMARK 500 SER A 70 -125.94 56.74 REMARK 500 PHE A 175 102.98 75.27 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: NESG-YER85 RELATED DB: TARGETTRACK DBREF 4FLE A 1 194 UNP A1JQU0 A1JQU0_YERE8 1 194 SEQADV 4FLE LEU A 195 UNP A1JQU0 EXPRESSION TAG SEQADV 4FLE GLU A 196 UNP A1JQU0 EXPRESSION TAG SEQADV 4FLE HIS A 197 UNP A1JQU0 EXPRESSION TAG SEQADV 4FLE HIS A 198 UNP A1JQU0 EXPRESSION TAG SEQADV 4FLE HIS A 199 UNP A1JQU0 EXPRESSION TAG SEQADV 4FLE HIS A 200 UNP A1JQU0 EXPRESSION TAG SEQADV 4FLE HIS A 201 UNP A1JQU0 EXPRESSION TAG SEQADV 4FLE HIS A 202 UNP A1JQU0 EXPRESSION TAG SEQRES 1 A 202 MSE MSE SER THR LEU LEU TYR ILE HIS GLY PHE ASN SER SEQRES 2 A 202 SER PRO SER SER ALA LYS ALA THR THR PHE LYS SER TRP SEQRES 3 A 202 LEU GLN GLN HIS HIS PRO HIS ILE GLU MSE GLN ILE PRO SEQRES 4 A 202 GLN LEU PRO PRO TYR PRO ALA GLU ALA ALA GLU MSE LEU SEQRES 5 A 202 GLU SER ILE VAL MSE ASP LYS ALA GLY GLN SER ILE GLY SEQRES 6 A 202 ILE VAL GLY SER SER LEU GLY GLY TYR PHE ALA THR TRP SEQRES 7 A 202 LEU SER GLN ARG PHE SER ILE PRO ALA VAL VAL VAL ASN SEQRES 8 A 202 PRO ALA VAL ARG PRO PHE GLU LEU LEU SER ASP TYR LEU SEQRES 9 A 202 GLY GLU ASN GLN ASN PRO TYR THR GLY GLN LYS TYR VAL SEQRES 10 A 202 LEU GLU SER ARG HIS ILE TYR ASP LEU LYS ALA MSE GLN SEQRES 11 A 202 ILE GLU LYS LEU GLU SER PRO ASP LEU LEU TRP LEU LEU SEQRES 12 A 202 GLN GLN THR GLY ASP GLU VAL LEU ASP TYR ARG GLN ALA SEQRES 13 A 202 VAL ALA TYR TYR THR PRO CYS ARG GLN THR VAL GLU SER SEQRES 14 A 202 GLY GLY ASN HIS ALA PHE VAL GLY PHE ASP HIS TYR PHE SEQRES 15 A 202 SER PRO ILE VAL THR PHE LEU GLY LEU ALA THR ALA LEU SEQRES 16 A 202 GLU HIS HIS HIS HIS HIS HIS MODRES 4FLE MSE A 36 MET SELENOMETHIONINE MODRES 4FLE MSE A 51 MET SELENOMETHIONINE MODRES 4FLE MSE A 57 MET SELENOMETHIONINE MODRES 4FLE MSE A 129 MET SELENOMETHIONINE HET MSE A 36 8 HET MSE A 51 8 HET MSE A 57 8 HET MSE A 129 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 4(C5 H11 N O2 SE) FORMUL 2 HOH *183(H2 O) HELIX 1 1 SER A 17 HIS A 31 1 15 HELIX 2 2 TYR A 44 ALA A 60 1 17 HELIX 3 3 LEU A 71 PHE A 83 1 13 HELIX 4 4 ARG A 95 LEU A 100 1 6 HELIX 5 5 SER A 101 LEU A 104 5 4 HELIX 6 6 GLU A 119 ALA A 128 1 10 HELIX 7 7 SER A 136 ASP A 138 5 3 HELIX 8 8 ASP A 152 TYR A 160 1 9 HELIX 9 9 GLY A 177 HIS A 180 5 4 HELIX 10 10 TYR A 181 GLY A 190 1 10 SHEET 1 A 6 GLU A 35 GLN A 37 0 SHEET 2 A 6 THR A 4 ILE A 8 1 N LEU A 5 O GLU A 35 SHEET 3 A 6 ILE A 64 SER A 69 1 O GLY A 65 N LEU A 6 SHEET 4 A 6 ALA A 87 VAL A 90 1 O VAL A 88 N ILE A 66 SHEET 5 A 6 LEU A 140 GLN A 145 1 O LEU A 143 N VAL A 89 SHEET 6 A 6 ARG A 164 GLU A 168 1 O GLU A 168 N GLN A 144 SHEET 1 B 2 GLY A 105 GLN A 108 0 SHEET 2 B 2 LYS A 115 LEU A 118 -1 O TYR A 116 N ASN A 107 LINK C GLU A 35 N MSE A 36 1555 1555 1.33 LINK C MSE A 36 N GLN A 37 1555 1555 1.33 LINK C GLU A 50 N MSE A 51 1555 1555 1.33 LINK C MSE A 51 N LEU A 52 1555 1555 1.33 LINK C VAL A 56 N MSE A 57 1555 1555 1.33 LINK C MSE A 57 N ASP A 58 1555 1555 1.33 LINK C ALA A 128 N MSE A 129 1555 1555 1.33 LINK C MSE A 129 N GLN A 130 1555 1555 1.33 CRYST1 55.056 79.543 46.060 90.00 90.00 90.00 P 21 21 2 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 0.018163 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012572 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021711 0.00000