HEADER HYDROLASE 08-NOV-22 8HEA TITLE ESTERASE2 (EAEST2) FROM EXIGUOBACTERIUM ANTARCTICUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: THERMOSTABLE CARBOXYLESTERASE EST30; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: EXIGUOBACTERIUM ANTARCTICUM B7; SOURCE 3 ORGANISM_TAXID: 1087448; SOURCE 4 GENE: EAB7_2224; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ESTERASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.HWANG,J.H.LEE REVDAT 1 20-SEP-23 8HEA 0 JRNL AUTH J.HWANG,W.YOO,S.C.SHIN,K.K.KIM,H.W.KIM,H.DO,J.H.LEE JRNL TITL STRUCTURAL AND BIOCHEMICAL INSIGHTS INTO BIS(2-HYDROXYETHYL) JRNL TITL 2 TEREPHTHALATE DEGRADING CARBOXYLESTERASE ISOLATED FROM JRNL TITL 3 PSYCHROTROPHIC BACTERIUM EXIGUOBACTERIUM ANTARCTICUM. JRNL REF INT J MOL SCI V. 24 2023 JRNL REFN ESSN 1422-0067 JRNL PMID 37569396 JRNL DOI 10.3390/IJMS241512022 REMARK 2 REMARK 2 RESOLUTION. 1.74 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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 : CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.74 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.70 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 32192 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 1619 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 31.7000 - 3.9800 1.00 2697 155 0.1747 0.1806 REMARK 3 2 3.9800 - 3.1600 1.00 2625 124 0.1844 0.1947 REMARK 3 3 3.1600 - 2.7600 1.00 2582 128 0.2075 0.2189 REMARK 3 4 2.7600 - 2.5100 1.00 2547 115 0.2034 0.2506 REMARK 3 5 2.5100 - 2.3300 1.00 2521 155 0.2051 0.2236 REMARK 3 6 2.3300 - 2.1900 1.00 2523 135 0.2083 0.2083 REMARK 3 7 2.1900 - 2.0800 1.00 2540 131 0.2072 0.2323 REMARK 3 8 2.0800 - 1.9900 1.00 2505 147 0.2060 0.2490 REMARK 3 9 1.9900 - 1.9100 1.00 2529 117 0.2113 0.2459 REMARK 3 10 1.9100 - 1.8500 1.00 2504 143 0.2016 0.2331 REMARK 3 11 1.8500 - 1.7900 1.00 2478 149 0.2263 0.2777 REMARK 3 12 1.7900 - 1.7400 1.00 2522 120 0.2307 0.2624 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.176 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.735 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.016 1977 REMARK 3 ANGLE : 1.781 2679 REMARK 3 CHIRALITY : 0.106 291 REMARK 3 PLANARITY : 0.011 347 REMARK 3 DIHEDRAL : 22.074 733 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 8HEA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-NOV-22. REMARK 100 THE DEPOSITION ID IS D_1300033473. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-MAY-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9796 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32327 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.740 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 53.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.74 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 1TQH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.78 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES:NAOH (PH 7.5), 20% (W/V) REMARK 280 PEG 8000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 296K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 25.18100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.80850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.89450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.80850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.18100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.89450 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 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 LYS A 2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 LYS A 7 C PRO A 8 N 0.143 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 THR A 25 -4.50 72.18 REMARK 500 SER A 93 -122.28 55.77 REMARK 500 ASN A 189 49.23 -95.53 REMARK 500 REMARK 500 REMARK: NULL DBREF 8HEA A 1 246 UNP K0AFS0 K0AFS0_EXIAB 1 246 SEQRES 1 A 246 MET LYS ILE THR LEU PRO LYS PRO PHE PHE PHE GLU GLY SEQRES 2 A 246 GLY ASN ARG ALA VAL LEU LEU LEU HIS GLY PHE THR GLY SEQRES 3 A 246 SER SER ALA ASP VAL ARG MET LEU GLY ARG TYR LEU GLN SEQRES 4 A 246 LYS HIS GLY TYR THR SER LEU ALA PRO GLN TYR LYS GLY SEQRES 5 A 246 HIS ALA ALA PRO PRO GLU GLU LEU THR LYS THR GLY PRO SEQRES 6 A 246 ALA ASP TRP TRP GLN ASP VAL LEU ASP GLY TYR GLU GLU SEQRES 7 A 246 LEU LYS ALA LYS GLY TYR ASP GLU ILE ALA VAL CYS GLY SEQRES 8 A 246 LEU SER LEU GLY GLY VAL MET SER LEU ARG LEU SER MET SEQRES 9 A 246 HIS ARG PRO VAL LYS ALA VAL ILE PRO MET CYS ALA PRO SEQRES 10 A 246 ALA TYR ILE LYS SER GLU ASP VAL MET TYR ALA GLY VAL SEQRES 11 A 246 THR GLU TYR ALA ARG GLU PHE LYS LYS ARG GLU GLY LYS SEQRES 12 A 246 SER VAL ASP GLU ILE GLU GLN GLU MET ALA VAL PHE GLU SEQRES 13 A 246 PRO MET PRO THR LEU LYS ASP LEU GLN ALA LEU LEU LYS SEQRES 14 A 246 GLU THR ARG ASP SER LEU GLU ASP VAL TYR ALA PRO THR SEQRES 15 A 246 LEU VAL VAL GLN ALA ARG ASN ASP HIS MET ILE ASN THR SEQRES 16 A 246 ASP SER ALA ASN ILE ILE HIS ASP GLY VAL SER ALA LEU SEQRES 17 A 246 GLN LYS GLU LEU ILE TRP TYR GLU ASN SER GLY HIS VAL SEQRES 18 A 246 ILE THR LEU ASP LYS GLU LYS GLU THR LEU HIS GLN ASP SEQRES 19 A 246 ILE HIS GLU PHE LEU ASP GLY LEU ASN TRP SER HIS FORMUL 2 HOH *169(H2 O) HELIX 1 AA1 SER A 27 ASP A 30 5 4 HELIX 2 AA2 VAL A 31 HIS A 41 1 11 HELIX 3 AA3 PRO A 56 THR A 61 1 6 HELIX 4 AA4 GLY A 64 LYS A 82 1 19 HELIX 5 AA5 SER A 93 ARG A 106 1 14 HELIX 6 AA6 SER A 122 GLU A 141 1 20 HELIX 7 AA7 SER A 144 VAL A 154 1 11 HELIX 8 AA8 THR A 160 SER A 174 1 15 HELIX 9 AA9 LEU A 175 VAL A 178 5 4 HELIX 10 AB1 ASP A 196 VAL A 205 1 10 HELIX 11 AB2 VAL A 221 ASP A 225 5 5 HELIX 12 AB3 GLU A 227 GLY A 241 1 15 SHEET 1 AA1 5 PHE A 9 PHE A 11 0 SHEET 2 AA1 5 THR A 44 ALA A 47 -1 O SER A 45 N PHE A 11 SHEET 3 AA1 5 ALA A 17 LEU A 21 1 N LEU A 20 O LEU A 46 SHEET 4 AA1 5 ILE A 87 LEU A 92 1 O ALA A 88 N LEU A 19 SHEET 5 AA1 5 VAL A 111 MET A 114 1 O MET A 114 N GLY A 91 SHEET 1 AA2 2 THR A 182 ALA A 187 0 SHEET 2 AA2 2 LYS A 210 TYR A 215 1 O GLU A 211 N VAL A 184 CRYST1 50.362 67.789 89.617 90.00 90.00 90.00 P 21 21 21 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 0.019856 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014752 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011159 0.00000