HEADER HYDROLASE 11-SEP-09 2WT5 OBSLTE 23-FEB-10 2WT5 TITLE STRUCTURE OF BETA-GLUCOSIDASE 3B FROM THERMOTOGA TITLE 2 NEAPOLITANA: MUTANT D242A IN COMPLEX WITH ALPHA-D-GLUCOSE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-GLUCOSIDASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BETA-GLUCOSIDASE 3B; COMPND 5 EC: 3.2.1.21; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA NEAPOLITANA; SOURCE 3 ORGANISM_TAXID: 309803; SOURCE 4 STRAIN: DSM 4359; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: TUNER(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET-22B; SOURCE 9 OTHER_DETAILS: GERMAN COLLECTION OF MICROORGANISMS (DSM) KEYWDS HYDROLASE, TIM BARREL FOLD, FIBRONECTIN TYPE III FOLD EXPDTA X-RAY DIFFRACTION AUTHOR T.POZZO,E.NORDBERG KARLSSON,D.T.LOGAN REVDAT 2 23-FEB-10 2WT5 1 OBSLTE REVDAT 1 16-FEB-10 2WT5 0 JRNL AUTH T.POZZO,J.LINARES PASTEN,E.NORDBERG KARLSSON, JRNL AUTH 2 D.T.LOGAN JRNL TITL STRUCTURAL AND FUNCTIONAL ANALYSIS OF BETA- JRNL TITL 2 GLUCOSIDASE 3B FROM THERMOTOGA NEAPOLITANA: A JRNL TITL 3 THERMOSTABLE 3-DOMAIN REPRESENTATIVE OF GLYCOSIDE JRNL TITL 4 HYDROLASE FAMILY 3 JRNL REF J.MOL.BIOL. 2010 JRNL REFN ESSN 1089-8638 JRNL PMID 20138890 JRNL DOI 10.1016/J.JMB.2010.01.072 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.TURNER,A.PRAMHED,E.KANDERS,M.HEDSTROM, REMARK 1 AUTH 2 E.N.KARLSSON,D.T.LOGAN REMARK 1 TITL EXPRESSION, PURIFICATION, CRYSTALLIZATION AND REMARK 1 TITL 2 PRELIMINARY X-RAY DIFFRACTION ANALYSIS OF REMARK 1 TITL 3 THERMOTOGA NEAPOLITANA BETA-GLUCOSIDASE B. REMARK 1 REF ACTA CRYSTALLOGR.,SECT.F V. 63 802 2007 REMARK 1 REFN ISSN 1744-3091 REMARK 1 PMID 17768360 REMARK 1 DOI 10.1107/S1744309107040341 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 2.101 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.250 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.35 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.26 REMARK 3 NUMBER OF REFLECTIONS : 44706 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.1842 REMARK 3 R VALUE (WORKING SET) : 0.1819 REMARK 3 FREE R VALUE : 0.2259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.0 REMARK 3 FREE R VALUE TEST SET COUNT : 2402 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 29.2528 - 5.3921 0.98 2853 173 0.1670 0.1949 REMARK 3 2 5.3921 - 4.2842 0.99 2802 149 0.1395 0.1831 REMARK 3 3 4.2842 - 3.7439 0.99 2771 146 0.1415 0.1618 REMARK 3 4 3.7439 - 3.4022 0.99 2760 131 0.1641 0.2120 REMARK 3 5 3.4022 - 3.1586 0.99 2766 147 0.1808 0.2330 REMARK 3 6 3.1586 - 2.9726 0.99 2713 134 0.2015 0.2396 REMARK 3 7 2.9726 - 2.8238 0.98 2734 152 0.1891 0.2526 REMARK 3 8 2.8238 - 2.7010 0.99 2697 144 0.1930 0.2398 REMARK 3 9 2.7010 - 2.5971 0.98 2708 143 0.1935 0.2457 REMARK 3 10 2.5971 - 2.5075 0.98 2667 141 0.2020 0.2863 REMARK 3 11 2.5075 - 2.4292 0.97 2693 143 0.2069 0.3024 REMARK 3 12 2.4292 - 2.3598 0.97 2675 143 0.2083 0.3086 REMARK 3 13 2.3598 - 2.2977 0.96 2596 140 0.2125 0.2777 REMARK 3 14 2.2977 - 2.2416 0.97 2636 136 0.2142 0.2873 REMARK 3 15 2.2416 - 2.1907 0.96 2633 126 0.2110 0.2476 REMARK 3 16 2.1907 - 2.1441 0.95 2612 138 0.2235 0.2438 REMARK 3 17 2.1441 - 2.1012 0.72 1969 116 0.2621 0.3204 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 : 0.374 REMARK 3 B_SOL : 50.698 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.12 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.19 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 32.76 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.7 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.2209 REMARK 3 B22 (A**2) : 1.6234 REMARK 3 B33 (A**2) : -1.4026 REMARK 3 B12 (A**2) : 0.0000 REMARK 3 B13 (A**2) : -0.0000 REMARK 3 B23 (A**2) : 0.0000 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 : 0.006 5815 REMARK 3 ANGLE : 1.008 7865 REMARK 3 CHIRALITY : 0.071 852 REMARK 3 PLANARITY : 0.004 1028 REMARK 3 DIHEDRAL : 18.060 2175 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 1:320) REMARK 3 ORIGIN FOR THE GROUP (A): -6.1624 24.9242 -21.9775 REMARK 3 T TENSOR REMARK 3 T11: 0.2330 T22: 0.1816 REMARK 3 T33: 0.1798 T12: -0.0396 REMARK 3 T13: 0.0048 T23: -0.0122 REMARK 3 L TENSOR REMARK 3 L11: 0.7637 L22: 0.7410 REMARK 3 L33: 0.9171 L12: 0.3638 REMARK 3 L13: -0.0572 L23: -0.0347 REMARK 3 S TENSOR REMARK 3 S11: -0.0114 S12: 0.0202 S13: 0.0499 REMARK 3 S21: -0.1528 S22: 0.0237 S23: -0.0307 REMARK 3 S31: -0.1990 S32: 0.1089 S33: -0.0141 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 321:536) REMARK 3 ORIGIN FOR THE GROUP (A): -39.2995 12.9821 -25.4314 REMARK 3 T TENSOR REMARK 3 T11: 0.1782 T22: 0.2715 REMARK 3 T33: 0.2829 T12: 0.0081 REMARK 3 T13: -0.1062 T23: 0.0079 REMARK 3 L TENSOR REMARK 3 L11: 0.3307 L22: 1.2199 REMARK 3 L33: 1.6078 L12: -0.2249 REMARK 3 L13: 0.4766 L23: 0.2725 REMARK 3 S TENSOR REMARK 3 S11: -0.0422 S12: -0.0619 S13: 0.0557 REMARK 3 S21: -0.1391 S22: 0.0270 S23: 0.3617 REMARK 3 S31: -0.1260 S32: -0.3658 S33: 0.0222 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 537:599) REMARK 3 ORIGIN FOR THE GROUP (A): -22.0522 5.8770 -8.6523 REMARK 3 T TENSOR REMARK 3 T11: 0.1867 T22: 0.2110 REMARK 3 T33: 0.2102 T12: -0.0048 REMARK 3 T13: -0.0077 T23: -0.0021 REMARK 3 L TENSOR REMARK 3 L11: 0.0580 L22: 0.1160 REMARK 3 L33: 0.2612 L12: -0.1976 REMARK 3 L13: 0.0371 L23: -0.2908 REMARK 3 S TENSOR REMARK 3 S11: -0.0082 S12: -0.0652 S13: -0.0225 REMARK 3 S21: 0.0355 S22: 0.0280 S23: 0.0987 REMARK 3 S31: 0.1055 S32: -0.1158 S33: -0.0233 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 600:721) REMARK 3 ORIGIN FOR THE GROUP (A): -10.0345 -8.3040 -20.3770 REMARK 3 T TENSOR REMARK 3 T11: 0.2582 T22: 0.2382 REMARK 3 T33: 0.2096 T12: 0.0167 REMARK 3 T13: 0.0090 T23: -0.0272 REMARK 3 L TENSOR REMARK 3 L11: 0.4764 L22: 1.0702 REMARK 3 L33: 0.4556 L12: -0.5110 REMARK 3 L13: 0.0293 L23: -0.5687 REMARK 3 S TENSOR REMARK 3 S11: 0.0691 S12: 0.0184 S13: -0.1693 REMARK 3 S21: -0.1644 S22: -0.0169 S23: -0.0539 REMARK 3 S31: 0.3264 S32: 0.1506 S33: -0.0027 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFMAC5 WAS USED PRIOR TO REMARK 3 PHENIX.REFINE. RESIDUES 1 AND 418-423 ARE DISORDERED. REMARK 4 REMARK 4 2WT5 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-SEP-09. REMARK 100 THE PDBE ID CODE IS EBI-41121. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-SEP-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MAX II REMARK 200 BEAMLINE : I911-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0379 REMARK 200 MONOCHROMATOR : BENT SI(111) CRYSTAL, REMARK 200 HORIZONTALLY FOCUSING REMARK 200 OPTICS : MULTILAYER MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44706 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.10 REMARK 200 RESOLUTION RANGE LOW (A) : 29.20 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 200 DATA REDUNDANCY : 4.6 REMARK 200 R MERGE (I) : 0.07 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.40 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) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.56 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.20 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: REFMAC5, PHENIX.REFINE REMARK 200 STARTING MODEL: PDB ENTRY 2WT3 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16-18 % PEG 3350, 0.2 M NABR, REMARK 280 90MM BIS-TRIS PROPANE PH 7.4. SOAKED IN ADDITIONAL 25% REMARK 280 GLYCEROL, 2% PEG 3350, 10 MM REMARK 280 PARANITROPHENYL-BETA-D-GLUCOSIDE FOR 30 MIN BEFORE DATA REMARK 280 COLLECTION 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 87.75000 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 87.75000 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 37.35000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 64.30000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 37.35000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 64.30000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 87.75000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 37.35000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 64.30000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 87.75000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 37.35000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 64.30000 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 GENERATING THE BIOMOLECULE 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, ASP 242 TO ALA 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 ASP A 418 REMARK 465 SER A 419 REMARK 465 TRP A 420 REMARK 465 GLY A 421 REMARK 465 THR A 422 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 2070 O HOH A 2085 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 2177 O HOH A 2198 4555 2.13 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 PHE A 29 -139.93 57.87 REMARK 500 MET A 120 28.41 -150.26 REMARK 500 VAL A 176 -36.44 -132.79 REMARK 500 ARG A 230 -64.11 -91.63 REMARK 500 ASN A 317 18.28 59.81 REMARK 500 ASN A 341 84.97 -155.65 REMARK 500 GLU A 362 57.95 -92.49 REMARK 500 ASN A 431 49.59 -100.59 REMARK 500 ASP A 468 -101.33 -126.32 REMARK 500 ASN A 498 69.75 -100.08 REMARK 500 TRP A 519 -136.74 49.12 REMARK 500 PRO A 539 126.76 -37.87 REMARK 500 ASN A 566 64.69 -159.73 REMARK 500 ASP A 575 -131.46 61.97 REMARK 500 GLU A 685 -50.79 -120.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 ALPHA-D-GLUCOSE (GLC): CRYSTAL SOAKED WITH PNPG, BETA REMARK 600 ANOMER, ALPHA-D-GLUCOSE FOUND IN THE ACTIVE SITE REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BR A1722 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BR A1723 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BR A1724 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BR A1725 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GLC A1726 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2WT3 RELATED DB: PDB REMARK 900 STRUCTURAL OF BETA-GLUCOSIDASE 3B FROM REMARK 900 THERMOTOGA NEAPOLITANA IN COMPLEX WITH GLUCOSE REMARK 900 : A THERMOSTABLE 3-DOMAIN REPRESENTATIVE OF REMARK 900 GLYCOSIDE HYDROLASE FAMILY 3 REMARK 900 RELATED ID: 2WT6 RELATED DB: PDB REMARK 900 STRUCTURAL OF BETA-GLUCOSIDASE 3B FROM REMARK 900 THERMOTOGA NEAPOLITANA IN COMPLEX WITH REMARK 900 GLYCEROL REMARK 900 RELATED ID: 2X41 RELATED DB: PDB REMARK 900 STRUCTURE OF BETA-GLUCOSIDASE 3B FROM REMARK 900 THERMOTOGA NEAPOLITANA IN COMPLEX WITH GLUCOSE REMARK 900 RELATED ID: 2X42 RELATED DB: PDB REMARK 900 STRUCTURE OF BETA-GLUCOSIDASE 3B FROM REMARK 900 THERMOTOGA NEAPOLITANA IN COMPLEX WITH ALPHA- REMARK 900 D-GLUCOSE REMARK 900 RELATED ID: 2X40 RELATED DB: PDB REMARK 900 STRUCTURE OF BETA-GLUCOSIDASE 3B FROM REMARK 900 THERMOTOGA NEAPOLITANA IN COMPLEX WITH REMARK 900 GLYCEROL REMARK 999 REMARK 999 SEQUENCE REMARK 999 MUTATION D242A DBREF 2WT5 A 1 721 UNP Q0GC07 Q0GC07_THENN 1 721 SEQADV 2WT5 ALA A 242 UNP Q0GC07 ASP 242 ENGINEERED MUTATION SEQRES 1 A 721 MET GLU LYS VAL ASN GLU ILE LEU SER GLN LEU THR LEU SEQRES 2 A 721 GLU GLU LYS VAL LYS LEU VAL VAL GLY VAL GLY LEU PRO SEQRES 3 A 721 GLY LEU PHE GLY ASN PRO HIS SER ARG VAL ALA GLY ALA SEQRES 4 A 721 ALA GLY GLU THR HIS PRO VAL PRO ARG VAL GLY LEU PRO SEQRES 5 A 721 ALA PHE VAL LEU ALA ASP GLY PRO ALA GLY LEU ARG ILE SEQRES 6 A 721 ASN PRO THR ARG GLU ASN ASP GLU ASN THR TYR TYR THR SEQRES 7 A 721 THR ALA PHE PRO VAL GLU ILE MET LEU ALA SER THR TRP SEQRES 8 A 721 ASN ARG GLU LEU LEU GLU GLU VAL GLY LYS ALA MET GLY SEQRES 9 A 721 GLU GLU VAL ARG GLU TYR GLY VAL ASP VAL LEU LEU ALA SEQRES 10 A 721 PRO ALA MET ASN ILE HIS ARG ASN PRO LEU CYS GLY ARG SEQRES 11 A 721 ASN PHE GLU TYR TYR SER GLU ASP PRO VAL LEU SER GLY SEQRES 12 A 721 GLU MET ALA SER SER PHE VAL LYS GLY VAL GLN SER GLN SEQRES 13 A 721 GLY VAL GLY ALA CYS ILE LYS HIS PHE VAL ALA ASN ASN SEQRES 14 A 721 GLN GLU THR ASN ARG MET VAL VAL ASP THR ILE VAL SER SEQRES 15 A 721 GLU ARG ALA LEU ARG GLU ILE TYR LEU ARG GLY PHE GLU SEQRES 16 A 721 ILE ALA VAL LYS LYS SER LYS PRO TRP SER VAL MET SER SEQRES 17 A 721 ALA TYR ASN LYS LEU ASN GLY LYS TYR CYS SER GLN ASN SEQRES 18 A 721 GLU TRP LEU LEU LYS LYS VAL LEU ARG GLU GLU TRP GLY SEQRES 19 A 721 PHE GLU GLY PHE VAL MET SER ALA TRP TYR ALA GLY ASP SEQRES 20 A 721 ASN PRO VAL GLU GLN LEU LYS ALA GLY ASN ASP LEU ILE SEQRES 21 A 721 MET PRO GLY LYS ALA TYR GLN VAL ASN THR GLU ARG ARG SEQRES 22 A 721 ASP GLU ILE GLU GLU ILE MET GLU ALA LEU LYS GLU GLY SEQRES 23 A 721 LYS LEU SER GLU GLU VAL LEU ASP GLU CYS VAL ARG ASN SEQRES 24 A 721 ILE LEU LYS VAL LEU VAL ASN ALA PRO SER PHE LYS ASN SEQRES 25 A 721 TYR ARG TYR SER ASN LYS PRO ASP LEU GLU LYS HIS ALA SEQRES 26 A 721 LYS VAL ALA TYR GLU ALA GLY ALA GLU GLY VAL VAL LEU SEQRES 27 A 721 LEU ARG ASN GLU GLU ALA LEU PRO LEU SER GLU ASN SER SEQRES 28 A 721 LYS ILE ALA LEU PHE GLY THR GLY GLN ILE GLU THR ILE SEQRES 29 A 721 LYS GLY GLY THR GLY SER GLY ASP THR HIS PRO ARG TYR SEQRES 30 A 721 ALA ILE SER ILE LEU GLU GLY ILE LYS GLU ARG GLY LEU SEQRES 31 A 721 ASN PHE ASP GLU GLU LEU ALA LYS THR TYR GLU ASP TYR SEQRES 32 A 721 ILE LYS LYS MET ARG GLU THR GLU GLU TYR LYS PRO ARG SEQRES 33 A 721 ARG ASP SER TRP GLY THR ILE ILE LYS PRO LYS LEU PRO SEQRES 34 A 721 GLU ASN PHE LEU SER GLU LYS GLU ILE HIS LYS LEU ALA SEQRES 35 A 721 LYS LYS ASN ASP VAL ALA VAL ILE VAL ILE SER ARG ILE SEQRES 36 A 721 SER GLY GLU GLY TYR ASP ARG LYS PRO VAL LYS GLY ASP SEQRES 37 A 721 PHE TYR LEU SER ASP ASP GLU THR ASP LEU ILE LYS THR SEQRES 38 A 721 VAL SER ARG GLU PHE HIS GLU GLN GLY LYS LYS VAL ILE SEQRES 39 A 721 VAL LEU LEU ASN ILE GLY SER PRO VAL GLU VAL VAL SER SEQRES 40 A 721 TRP ARG ASP LEU VAL ASP GLY ILE LEU LEU VAL TRP GLN SEQRES 41 A 721 ALA GLY GLN GLU THR GLY ARG ILE VAL ALA ASP VAL LEU SEQRES 42 A 721 THR GLY ARG ILE ASN PRO SER GLY LYS LEU PRO THR THR SEQRES 43 A 721 PHE PRO ARG ASP TYR SER ASP VAL PRO SER TRP THR PHE SEQRES 44 A 721 PRO GLY GLU PRO LYS ASP ASN PRO GLN LYS VAL VAL TYR SEQRES 45 A 721 GLU GLU ASP ILE TYR VAL GLY TYR ARG TYR TYR ASP THR SEQRES 46 A 721 PHE GLY VAL GLU PRO ALA TYR GLU PHE GLY TYR GLY LEU SEQRES 47 A 721 SER TYR THR THR PHE GLU TYR SER ASP LEU ASN VAL SER SEQRES 48 A 721 PHE ASP GLY GLU THR LEU ARG VAL GLN TYR ARG ILE GLU SEQRES 49 A 721 ASN THR GLY GLY ARG ALA GLY LYS GLU VAL SER GLN VAL SEQRES 50 A 721 TYR ILE LYS ALA PRO LYS GLY LYS ILE ASP LYS PRO PHE SEQRES 51 A 721 GLN GLU LEU LYS ALA PHE HIS LYS THR ARG LEU LEU ASN SEQRES 52 A 721 PRO GLY GLU SER GLU GLU VAL VAL LEU GLU ILE PRO VAL SEQRES 53 A 721 ARG ASP LEU ALA SER PHE ASN GLY GLU GLU TRP VAL VAL SEQRES 54 A 721 GLU ALA GLY GLU TYR GLU VAL ARG VAL GLY ALA SER SER SEQRES 55 A 721 ARG ASN ILE LYS LEU LYS GLY THR PHE SER VAL GLY GLU SEQRES 56 A 721 GLU ARG ARG PHE LYS PRO HET BR A1722 1 HET BR A1723 1 HET BR A1724 1 HET BR A1725 1 HET GLC A1726 12 HETNAM GLC ALPHA-D-GLUCOSE HETNAM BR BROMIDE ION FORMUL 3 GLC C6 H12 O6 FORMUL 4 BR 4(BR 1-) FORMUL 5 HOH *258(H2 O) HELIX 1 1 GLU A 2 LEU A 11 1 10 HELIX 2 2 THR A 12 VAL A 20 1 9 HELIX 3 3 VAL A 83 THR A 90 1 8 HELIX 4 4 ASN A 92 VAL A 99 1 8 HELIX 5 5 GLU A 105 TYR A 110 1 6 HELIX 6 6 ARG A 130 TYR A 134 5 5 HELIX 7 7 GLU A 144 LYS A 151 1 8 HELIX 8 8 SER A 182 ILE A 189 1 8 HELIX 9 9 PHE A 194 LYS A 202 1 9 HELIX 10 10 CYS A 218 GLN A 220 5 3 HELIX 11 11 ASN A 221 LYS A 226 1 6 HELIX 12 12 LYS A 227 TRP A 233 1 7 HELIX 13 13 ASN A 248 ALA A 255 1 8 HELIX 14 14 LYS A 264 VAL A 268 5 5 HELIX 15 15 ASP A 274 GLU A 285 1 12 HELIX 16 16 SER A 289 VAL A 305 1 17 HELIX 17 17 ASN A 306 ASN A 312 5 7 HELIX 18 18 ASP A 320 ALA A 331 1 12 HELIX 19 19 ASP A 393 THR A 410 1 18 HELIX 20 20 SER A 434 ASN A 445 1 12 HELIX 21 21 SER A 472 GLN A 489 1 18 HELIX 22 22 TRP A 508 VAL A 512 5 5 HELIX 23 23 ARG A 527 THR A 534 1 8 HELIX 24 24 ASP A 550 VAL A 554 5 5 HELIX 25 25 TYR A 580 PHE A 586 1 7 HELIX 26 26 ARG A 677 ALA A 680 5 4 SHEET 1 AA 2 LEU A 56 ALA A 57 0 SHEET 2 AA 2 VAL A 114 LEU A 115 1 O VAL A 114 N ALA A 57 SHEET 1 AB 3 CYS A 161 PHE A 165 0 SHEET 2 AB 3 SER A 205 SER A 208 1 O SER A 205 N ILE A 162 SHEET 3 AB 3 VAL A 239 SER A 241 1 O MET A 240 N SER A 208 SHEET 1 AC 3 LYS A 212 LEU A 213 0 SHEET 2 AC 3 ASP A 178 ILE A 180 1 N THR A 179 O LYS A 212 SHEET 3 AC 3 LYS A 569 VAL A 571 1 O VAL A 570 N ILE A 180 SHEET 1 AD 5 VAL A 337 LEU A 338 0 SHEET 2 AD 5 LEU A 516 LEU A 517 -1 O LEU A 517 N VAL A 337 SHEET 3 AD 5 LYS A 492 ASN A 498 1 O VAL A 495 N LEU A 516 SHEET 4 AD 5 VAL A 447 SER A 453 1 O ALA A 448 N ILE A 494 SHEET 5 AD 5 ILE A 353 LEU A 355 1 O ALA A 354 N VAL A 449 SHEET 1 AE 2 PHE A 547 PRO A 548 0 SHEET 2 AE 2 PRO A 590 TYR A 592 -1 N ALA A 591 O PHE A 547 SHEET 1 AF 3 PHE A 603 PHE A 612 0 SHEET 2 AF 3 THR A 616 ASN A 625 -1 O ARG A 618 N SER A 611 SHEET 3 AF 3 SER A 667 PRO A 675 -1 O GLU A 668 N ILE A 623 SHEET 1 AG 4 GLU A 652 LYS A 658 0 SHEET 2 AG 4 VAL A 634 LYS A 640 -1 O SER A 635 N HIS A 657 SHEET 3 AG 4 GLU A 695 SER A 701 -1 O GLU A 695 N LYS A 640 SHEET 4 AG 4 ASN A 704 LEU A 707 -1 O ASN A 704 N SER A 701 SHEET 1 AH 3 SER A 681 PHE A 682 0 SHEET 2 AH 3 TRP A 687 VAL A 689 -1 O VAL A 688 N SER A 681 SHEET 3 AH 3 ARG A 717 PHE A 719 -1 O ARG A 717 N VAL A 689 CISPEP 1 ASP A 58 GLY A 59 0 4.21 CISPEP 2 ALA A 117 PRO A 118 0 4.69 CISPEP 3 LYS A 163 HIS A 164 0 -7.43 CISPEP 4 PHE A 165 VAL A 166 0 2.70 CISPEP 5 MET A 261 PRO A 262 0 -2.41 CISPEP 6 LEU A 345 PRO A 346 0 0.75 CISPEP 7 PHE A 559 PRO A 560 0 1.90 CISPEP 8 GLU A 562 PRO A 563 0 -6.48 SITE 1 AC1 2 ARG A 340 TYR A 592 SITE 1 AC2 3 SER A 456 GLY A 500 SER A 501 SITE 1 AC3 5 ASN A 121 ILE A 122 ALA A 167 ASN A 169 SITE 2 AC3 5 TYR A 190 SITE 1 AC4 3 THR A 558 VAL A 571 HOH A2183 SITE 1 AC5 12 ASP A 58 LEU A 116 ARG A 130 LYS A 163 SITE 2 AC5 12 HIS A 164 ARG A 174 MET A 207 TYR A 210 SITE 3 AC5 12 ALA A 242 TRP A 243 SER A 370 GLU A 458 CRYST1 74.700 128.600 175.500 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 0.013387 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007776 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005698 0.00000