HEADER HYDROLASE 17-JUN-04 1TQH TITLE COVALENT REACTION INTERMEDIATE REVEALED IN CRYSTAL STRUCTURE OF THE TITLE 2 GEOBACILLUS STEAROTHERMOPHILUS CARBOXYLESTERASE EST30 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CARBOXYLESTERASE PRECURSOR; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.1.1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS STEAROTHERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 1422; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CARBOXYLESTERASE, TETRAHEDRAL INTERMEDIATE, ALPHA/BETA HYDROLASE, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR P.LIU,Y.F.WANG,H.E.EWIS,A.T.ABDELAL,C.D.LU,R.W.HARRISON,I.T.WEBER REVDAT 5 06-NOV-24 1TQH 1 REMARK LINK REVDAT 4 11-OCT-17 1TQH 1 REMARK REVDAT 3 30-APR-14 1TQH 1 REMARK VERSN REVDAT 2 24-FEB-09 1TQH 1 VERSN REVDAT 1 28-SEP-04 1TQH 0 JRNL AUTH P.LIU,Y.F.WANG,H.E.EWIS,A.T.ABDELAL,C.D.LU,R.W.HARRISON, JRNL AUTH 2 I.T.WEBER JRNL TITL COVALENT REACTION INTERMEDIATE REVEALED IN CRYSTAL STRUCTURE JRNL TITL 2 OF THE GEOBACILLUS STEAROTHERMOPHILUS CARBOXYLESTERASE JRNL TITL 3 EST30. JRNL REF J.MOL.BIOL. V. 342 551 2004 JRNL REFN ISSN 0022-2836 JRNL PMID 15327954 JRNL DOI 10.1016/J.JMB.2004.06.069 REMARK 2 REMARK 2 RESOLUTION. 1.63 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.63 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.171 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.168 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1768 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 35376 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.164 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.161 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 1581 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 31675 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1959 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 17 REMARK 3 SOLVENT ATOMS : 153 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 2115.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 9 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 19536 REMARK 3 NUMBER OF RESTRAINTS : 24598 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 ANGLE DISTANCES (A) : 0.024 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.025 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.038 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.051 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.011 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.002 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.038 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.087 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1TQH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JUL-04. REMARK 100 THE DEPOSITION ID IS D_1000022838. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-OCT-03; 06-MAR-03 REMARK 200 TEMPERATURE (KELVIN) : 95; 95 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : APS; APS REMARK 200 BEAMLINE : 22-ID; 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99997; 0.97920, 0.97933, REMARK 200 0.971602, 0.987072 REMARK 200 MONOCHROMATOR : SI; SI REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD; MAR CCD REMARK 200 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36452 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.630 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.15500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.63 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.5 REMARK 200 DATA REDUNDANCY IN SHELL : 6.20 REMARK 200 R MERGE FOR SHELL (I) : 0.18100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 14.30 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE, RESOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: LITHIUM SULFATE, PEG400, DIOXANE, REMARK 280 HEPES, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 297K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z 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 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 89.52250 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 89.52250 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 27.82700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 29.10250 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 27.82700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 29.10250 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 89.52250 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 27.82700 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 29.10250 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 89.52250 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 27.82700 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 29.10250 REMARK 290 SMTRY3 8 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 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 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 MET A 2 REMARK 465 LYS A 3 REMARK 465 ILE A 4 REMARK 465 VAL A 5 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 ARG A 136 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 191 NE - CZ - NH1 ANGL. DEV. = 3.2 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 ALA A 14 -40.75 -149.24 REMARK 500 THR A 26 -1.83 75.68 REMARK 500 SER A 94 -120.65 57.69 REMARK 500 GLN A 158 28.00 -79.15 REMARK 500 HIS A 192 61.25 -107.29 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 SO4 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 4PA A 701 DBREF 1TQH A 1 247 UNP Q06174 EST_BACST 1 247 SEQRES 1 A 247 MET MET LYS ILE VAL PRO PRO LYS PRO PHE PHE PHE GLU SEQRES 2 A 247 ALA GLY GLU ARG ALA VAL LEU LEU LEU HIS GLY PHE THR SEQRES 3 A 247 GLY ASN SER ALA ASP VAL ARG MET LEU GLY ARG PHE LEU SEQRES 4 A 247 GLU SER LYS GLY TYR THR CYS HIS ALA PRO ILE TYR LYS SEQRES 5 A 247 GLY HIS GLY VAL PRO PRO GLU GLU LEU VAL HIS THR GLY SEQRES 6 A 247 PRO ASP ASP TRP TRP GLN ASP VAL MET ASN GLY TYR GLU SEQRES 7 A 247 PHE LEU LYS ASN LYS GLY TYR GLU LYS ILE ALA VAL ALA SEQRES 8 A 247 GLY LEU SER LEU GLY GLY VAL PHE SER LEU LYS LEU GLY SEQRES 9 A 247 TYR THR VAL PRO ILE GLU GLY ILE VAL THR MET CYS ALA SEQRES 10 A 247 PRO MET TYR ILE LYS SER GLU GLU THR MET TYR GLU GLY SEQRES 11 A 247 VAL LEU GLU TYR ALA ARG GLU TYR LYS LYS ARG GLU GLY SEQRES 12 A 247 LYS SER GLU GLU GLN ILE GLU GLN GLU MET GLU LYS PHE SEQRES 13 A 247 LYS GLN THR PRO MET LYS THR LEU LYS ALA LEU GLN GLU SEQRES 14 A 247 LEU ILE ALA ASP VAL ARG ASP HIS LEU ASP LEU ILE TYR SEQRES 15 A 247 ALA PRO THR PHE VAL VAL GLN ALA ARG HIS ASP GLU MET SEQRES 16 A 247 ILE ASN PRO ASP SER ALA ASN ILE ILE TYR ASN GLU ILE SEQRES 17 A 247 GLU SER PRO VAL LYS GLN ILE LYS TRP TYR GLU GLN SER SEQRES 18 A 247 GLY HIS VAL ILE THR LEU ASP GLN GLU LYS ASP GLN LEU SEQRES 19 A 247 HIS GLU ASP ILE TYR ALA PHE LEU GLU SER LEU ASP TRP HET SO4 A 501 5 HET SO4 A 502 5 HET 4PA A 701 7 HETNAM SO4 SULFATE ION HETNAM 4PA PROPYL ACETATE FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 4PA C5 H10 O2 FORMUL 5 HOH *153(H2 O) HELIX 1 1 SER A 29 LYS A 42 1 14 HELIX 2 2 PRO A 57 VAL A 62 1 6 HELIX 3 3 GLY A 65 LYS A 83 1 19 HELIX 4 4 SER A 94 TYR A 105 1 12 HELIX 5 5 SER A 123 GLY A 143 1 21 HELIX 6 6 SER A 145 LYS A 157 1 13 HELIX 7 7 THR A 163 HIS A 177 1 15 HELIX 8 8 LEU A 178 ILE A 181 5 4 HELIX 9 9 ASP A 199 ILE A 208 1 10 HELIX 10 10 VAL A 224 ASP A 228 5 5 HELIX 11 11 GLU A 230 LEU A 245 1 16 SHEET 1 A 7 PHE A 10 PHE A 12 0 SHEET 2 A 7 THR A 45 ALA A 48 -1 O CYS A 46 N PHE A 12 SHEET 3 A 7 ALA A 18 LEU A 22 1 N LEU A 21 O HIS A 47 SHEET 4 A 7 ILE A 88 LEU A 93 1 O ALA A 91 N LEU A 20 SHEET 5 A 7 ILE A 112 MET A 115 1 O MET A 115 N GLY A 92 SHEET 6 A 7 THR A 185 ALA A 190 1 O VAL A 188 N THR A 114 SHEET 7 A 7 LYS A 213 TYR A 218 1 O GLN A 214 N VAL A 187 LINK OG SER A 94 CAI 4PA A 701 1555 1555 1.44 SITE 1 AC1 5 LYS A 83 SER A 123 GLU A 124 GLN A 168 SITE 2 AC1 5 HOH A1099 SITE 1 AC2 4 ARG A 33 ARG A 37 HOH A1062 HOH A1137 SITE 1 AC3 9 GLY A 24 PHE A 25 GLY A 27 ASP A 31 SITE 2 AC3 9 SER A 94 LEU A 95 HIS A 223 HOH A1070 SITE 3 AC3 9 HOH A1073 CRYST1 55.654 58.205 179.045 90.00 90.00 90.00 C 2 2 21 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 0.017968 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017181 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005585 0.00000