HEADER HYDROLASE 10-APR-00 1E0X TITLE XYLANASE 10A FROM SREPTOMYCES LIVIDANS. XYLOBIOSYL-ENZYME INTERMEDIATE TITLE 2 AT 1.65 A COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDO-1,4-BETA-XYLANASE A; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CATALYTIC MODULE, RESIDUES 32-450; COMPND 5 SYNONYM: XYLANASE A, 1,4-BETA-D-XYLAN XYLANOHYDROLASE A; COMPND 6 EC: 3.2.1.8; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: GLYCOSYL ENXYME INTERMEDIATE. COVALENT LINK BETWEEN COMPND 9 GLU 236 AND THE SUBSTRATE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES LIVIDANS; SOURCE 3 ORGANISM_TAXID: 1916; SOURCE 4 EXPRESSION_SYSTEM: STREPTOMYCES LIVIDANS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 1916; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: IAF 19 KEYWDS GLYCOSIDE HYDROLASE FAMILY 10, HYDROLASE, XYLAN DEGRADATION, KEYWDS 2 GLYCOSYL-ENZYME INTERMEDIATE EXPDTA X-RAY DIFFRACTION AUTHOR V.DUCROS,S.J.CHARNOCK,U.DEREWENDA,Z.S.DEREWENDA,Z.DAUTER,C.DUPONT, AUTHOR 2 F.SHARECK,R.MOROSOLI,D.KLUEPFEL,G.J.DAVIES REVDAT 8 13-NOV-24 1E0X 1 REMARK REVDAT 7 01-MAY-24 1E0X 1 HETSYN REVDAT 6 29-JUL-20 1E0X 1 COMPND REMARK HETNAM LINK REVDAT 6 2 1 SITE ATOM REVDAT 5 31-AUG-11 1E0X 1 HEADER COMPND KEYWDS REMARK REVDAT 5 2 1 HETSYN FORMUL SITE ATOM REVDAT 5 3 1 TER HETATM VERSN REVDAT 4 24-FEB-09 1E0X 1 VERSN REVDAT 3 24-JUN-03 1E0X 1 COMPND REMARK HET HETNAM REVDAT 3 2 1 FORMUL ATOM TER HETATM REVDAT 2 25-MAY-01 1E0X 1 JRNL REMARK REVDAT 1 05-APR-01 1E0X 0 JRNL AUTH V.DUCROS,S.J.CHARNOCK,U.DEREWENDA,Z.S.DEREWENDA,Z.DAUTER, JRNL AUTH 2 C.DUPONT,F.SHARECK,R.MOROSOLI,D.KLUEPFEL,G.J.DAVIES JRNL TITL SUBSTRATE SPECIFICITY IN GLYCOSIDE HYDROLASE FAMILY 10. JRNL TITL 2 STRUCTURAL AND KINETIC ANALYSIS OF THE STREPTOMYCES LIVIDANS JRNL TITL 3 XYLANASE 10A JRNL REF J.BIOL.CHEM. V. 275 23020 2000 JRNL REFN ISSN 0021-9258 JRNL PMID 10930426 JRNL DOI 10.1074/JBC.M000129200 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH U.DEREWENDA,L.SWENSON,R.GREEN,Y.WEI,R.MOROSOLI,F.SHARECK, REMARK 1 AUTH 2 D.KLUEPFEL,Z.S.DEREWENDA REMARK 1 TITL CRYSTAL STRUCTURE, AT 2.6 A RESOLUTION, OF THE STREPTOMYCES REMARK 1 TITL 2 LIVIDANS XYLANASE A, A MEMBER OF THE F FAMILY OF REMARK 1 TITL 3 B-1,4-D-GLYCANASES REMARK 1 REF J.BIOL.CHEM. V. 269 20811 1994 REMARK 1 REFN ISSN 0021-9258 REMARK 1 PMID 8063693 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 63415 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 + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.126 REMARK 3 FREE R VALUE : 0.162 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3381 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4760 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 54 REMARK 3 SOLVENT ATOMS : 717 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.012 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.028 ; 0.040 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.034 ; 0.050 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.026 ; 0.030 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.121 ; 0.150 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.160 ; 0.300 REMARK 3 MULTIPLE TORSION (A) : 0.260 ; 0.300 REMARK 3 H-BOND (X...Y) (A) : 0.140 ; 0.300 REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : 4.700 ; 7.000 REMARK 3 STAGGERED (DEGREES) : 12.300; 15.000 REMARK 3 TRANSVERSE (DEGREES) : 27.800; 20.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.448 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.994 ; 5.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.301 ; 4.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.885 ; 6.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: DOUBLY CONFIGURATED DISULPHIDE BOND REMARK 3 BETWEEN CYS168 AND CYS201 REMARK 4 REMARK 4 1E0X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-APR-00. REMARK 100 THE DEPOSITION ID IS D_1290004843. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-NOV-97 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.50 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : LONG MIRRORS (MSC) REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 66881 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.03300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 35.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : 0.09700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 12.90 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NATIVE STRUCTURE AT 1.2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN WAS CRYSTALLISED WITH 18 % PEG REMARK 280 5000 AS PRECIPITANT, 100MM HEPES PH 7.5 AS BUFFER, 10% REMARK 280 ISOPROPANOL, CRYSTAL WERE SOAKED IN PRESENCE OF POWDERED REMARK 280 SUBSTRATE FOR 12 HOURS. 15% GLYCEROL WAS ADDED AS CRYOPROTECTANT, REMARK 280 PH 7.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 40.53000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 REMARK 350 BIOMOLECULE: 2 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: B, D 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 ASP A 311 REMARK 465 GLY A 312 REMARK 465 GLY A 313 REMARK 465 ASP B 311 REMARK 465 GLY B 312 REMARK 465 GLY B 313 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ALA A 310 CA C O CB REMARK 470 ALA B 310 CA C O CB 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 C GLU B 277 O HOH B 506 0.42 REMARK 500 OG SER B 164 O HOH B 501 0.51 REMARK 500 CA ALA A 160 O HOH A 502 0.64 REMARK 500 CA ALA B 292 O HOH B 507 0.68 REMARK 500 CB ALA A 100 O HOH A 787 0.78 REMARK 500 OG1 THR B 279 O HOH B 502 0.79 REMARK 500 CG ASP B 162 O HOH B 509 0.98 REMARK 500 O ARG B 159 O HOH B 503 1.05 REMARK 500 O SER B 276 O HOH B 504 1.15 REMARK 500 CB ASP B 162 O HOH B 509 1.17 REMARK 500 CB ALA B 292 O HOH B 507 1.22 REMARK 500 N ASN B 215 O HOH B 505 1.24 REMARK 500 CA GLU B 277 O HOH B 506 1.27 REMARK 500 CA ASN A 60 O HOH A 501 1.36 REMARK 500 O GLU B 277 O HOH B 506 1.39 REMARK 500 C ALA A 160 O HOH A 502 1.42 REMARK 500 N ALA B 292 O HOH B 507 1.47 REMARK 500 C GLN B 278 O HOH B 508 1.48 REMARK 500 O GLN B 278 O HOH B 508 1.49 REMARK 500 CA ASN B 215 O HOH B 505 1.49 REMARK 500 OD1 ASP B 162 O HOH B 509 1.50 REMARK 500 CG2 ILE B 239 O HOH B 801 1.51 REMARK 500 O ALA B 160 O HOH B 510 1.51 REMARK 500 C PRO B 163 O HOH B 514 1.54 REMARK 500 N GLN B 278 O HOH B 506 1.55 REMARK 500 CB ASN B 215 O HOH B 505 1.56 REMARK 500 N SER B 271 O HOH B 511 1.58 REMARK 500 NE2 GLN B 11 O HOH B 512 1.62 REMARK 500 O PHE A 59 O HOH A 501 1.62 REMARK 500 C SER B 276 O HOH B 504 1.63 REMARK 500 CD1 LEU A 96 O HOH A 511 1.63 REMARK 500 CA SER B 271 O HOH B 511 1.64 REMARK 500 CB SER B 164 O HOH B 501 1.70 REMARK 500 CB ALA A 160 O HOH A 502 1.73 REMARK 500 N GLN B 278 O HOH B 513 1.74 REMARK 500 N ASN A 60 O HOH A 501 1.79 REMARK 500 CB SER B 164 O HOH B 501 1.81 REMARK 500 CA GLN B 278 O HOH B 513 1.84 REMARK 500 CB PRO B 163 O HOH B 514 1.85 REMARK 500 CA GLN B 278 O HOH B 508 1.85 REMARK 500 CA ASP B 162 O HOH B 509 1.88 REMARK 500 CG GLN B 278 O HOH B 513 1.89 REMARK 500 C PHE A 59 O HOH A 501 1.90 REMARK 500 CB SER B 164 O HOH B 515 1.94 REMARK 500 CD GLN B 11 O HOH B 512 1.95 REMARK 500 OE1 GLN B 11 O HOH B 512 1.96 REMARK 500 CD PRO B 198 O HOH B 516 1.96 REMARK 500 CA PRO B 163 O HOH B 514 1.96 REMARK 500 CB THR B 279 O HOH B 502 1.97 REMARK 500 C ASP B 270 O HOH B 511 1.99 REMARK 500 REMARK 500 THIS ENTRY HAS 61 CLOSE CONTACTS 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 OG SER B 97 O HOH B 512 2647 2.04 REMARK 500 REMARK 500 REMARK: NULL 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 GLU A 236 CD GLU A 236 OE1 0.119 REMARK 500 GLU B 236 CD GLU B 236 OE1 0.112 REMARK 500 REMARK 500 REMARK: NULL 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 36 CD - NE - CZ ANGL. DEV. = 15.8 DEGREES REMARK 500 ASP A 50 CB - CG - OD1 ANGL. DEV. = 8.2 DEGREES REMARK 500 ARG A 56 NE - CZ - NH2 ANGL. DEV. = 6.4 DEGREES REMARK 500 ARG A 56 NE - CZ - NH2 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG A 66 CD - NE - CZ ANGL. DEV. = 30.7 DEGREES REMARK 500 ARG A 66 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG A 66 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 79 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 79 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ASP A 132 N - CA - CB ANGL. DEV. = 17.3 DEGREES REMARK 500 ASP A 132 CB - CG - OD1 ANGL. DEV. = 6.3 DEGREES REMARK 500 ASP A 132 CB - CG - OD2 ANGL. DEV. = -10.6 DEGREES REMARK 500 ASP A 132 CB - CG - OD2 ANGL. DEV. = 10.0 DEGREES REMARK 500 ARG A 138 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A 159 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 159 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 ARG A 195 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG A 195 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 CYS A 201 CA - CB - SG ANGL. DEV. = 10.8 DEGREES REMARK 500 CYS A 201 CA - CB - SG ANGL. DEV. = 13.8 DEGREES REMARK 500 GLU B 2 OE1 - CD - OE2 ANGL. DEV. = 11.0 DEGREES REMARK 500 ARG B 36 CD - NE - CZ ANGL. DEV. = 10.5 DEGREES REMARK 500 ARG B 56 NE - CZ - NH2 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP B 132 CB - CG - OD2 ANGL. DEV. = -9.0 DEGREES REMARK 500 ARG B 145 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG B 159 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 PHE B 192 CB - CG - CD2 ANGL. DEV. = -4.7 DEGREES REMARK 500 ARG B 195 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 CYS B 201 CA - CB - SG ANGL. DEV. = 8.2 DEGREES REMARK 500 CYS B 201 CA - CB - SG ANGL. DEV. = 11.4 DEGREES REMARK 500 SER B 212 CA - CB - OG ANGL. DEV. = 16.4 DEGREES REMARK 500 SER B 258 CA - CB - OG ANGL. DEV. = 22.3 DEGREES REMARK 500 ARG B 269 NE - CZ - NH2 ANGL. DEV. = -3.5 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 ASN A 45 -15.37 -142.50 REMARK 500 GLN A 58 78.16 -115.85 REMARK 500 GLU A 236 38.70 -142.60 REMARK 500 VAL A 268 -75.63 -100.95 REMARK 500 THR A 279 66.80 31.87 REMARK 500 ASN B 45 -15.61 -142.43 REMARK 500 GLN B 58 74.69 -104.44 REMARK 500 ASP B 149 3.46 -68.80 REMARK 500 GLU B 236 40.67 -140.91 REMARK 500 VAL B 268 -76.71 -101.51 REMARK 500 THR B 279 66.85 28.44 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1XAS RELATED DB: PDB REMARK 900 XYLANASE A REMARK 900 RELATED ID: 1E0V RELATED DB: PDB REMARK 900 XYLANASE 10A FROM SREPTOMYCES LIVIDANS. CELLOBIOSYL-ENZYME REMARK 900 INTERMEDIATE AT 1.7 A REMARK 900 RELATED ID: 1E0W RELATED DB: PDB REMARK 900 XYLANASE 10A FROM SREPTOMYCES LIVIDANS. NATIVE STRUCTURE AT 1.2 REMARK 900 ANGSTROM RESOLUTION REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE FIRST 41 RESIDUES IN THE DATABASE CORRESPOND REMARK 999 TO THE SIGNAL PEPTIDE. THE NUMBERING USED IN THE PDB FILE REMARK 999 IF AFTER CLEAVAGE OF THE SIGNAL PEPTIDE. REMARK 999 THE LAST 4 RESIDUES ARE INVISIBLE IN DENSITY. DBREF 1E0X A 1 309 UNP P26514 XYNA_STRLI 42 350 DBREF 1E0X B 1 309 UNP P26514 XYNA_STRLI 42 350 SEQRES 1 A 313 ALA GLU SER THR LEU GLY ALA ALA ALA ALA GLN SER GLY SEQRES 2 A 313 ARG TYR PHE GLY THR ALA ILE ALA SER GLY ARG LEU SER SEQRES 3 A 313 ASP SER THR TYR THR SER ILE ALA GLY ARG GLU PHE ASN SEQRES 4 A 313 MET VAL THR ALA GLU ASN GLU MET LYS ILE ASP ALA THR SEQRES 5 A 313 GLU PRO GLN ARG GLY GLN PHE ASN PHE SER SER ALA ASP SEQRES 6 A 313 ARG VAL TYR ASN TRP ALA VAL GLN ASN GLY LYS GLN VAL SEQRES 7 A 313 ARG GLY HIS THR LEU ALA TRP HIS SER GLN GLN PRO GLY SEQRES 8 A 313 TRP MET GLN SER LEU SER GLY SER ALA LEU ARG GLN ALA SEQRES 9 A 313 MET ILE ASP HIS ILE ASN GLY VAL MET ALA HIS TYR LYS SEQRES 10 A 313 GLY LYS ILE VAL GLN TRP ASP VAL VAL ASN GLU ALA PHE SEQRES 11 A 313 ALA ASP GLY SER SER GLY ALA ARG ARG ASP SER ASN LEU SEQRES 12 A 313 GLN ARG SER GLY ASN ASP TRP ILE GLU VAL ALA PHE ARG SEQRES 13 A 313 THR ALA ARG ALA ALA ASP PRO SER ALA LYS LEU CYS TYR SEQRES 14 A 313 ASN ASP TYR ASN VAL GLU ASN TRP THR TRP ALA LYS THR SEQRES 15 A 313 GLN ALA MET TYR ASN MET VAL ARG ASP PHE LYS GLN ARG SEQRES 16 A 313 GLY VAL PRO ILE ASP CYS VAL GLY PHE GLN SER HIS PHE SEQRES 17 A 313 ASN SER GLY SER PRO TYR ASN SER ASN PHE ARG THR THR SEQRES 18 A 313 LEU GLN ASN PHE ALA ALA LEU GLY VAL ASP VAL ALA ILE SEQRES 19 A 313 THR GLU LEU ASP ILE GLN GLY ALA PRO ALA SER THR TYR SEQRES 20 A 313 ALA ASN VAL THR ASN ASP CYS LEU ALA VAL SER ARG CYS SEQRES 21 A 313 LEU GLY ILE THR VAL TRP GLY VAL ARG ASP SER ASP SER SEQRES 22 A 313 TRP ARG SER GLU GLN THR PRO LEU LEU PHE ASN ASN ASP SEQRES 23 A 313 GLY SER LYS LYS ALA ALA TYR THR ALA VAL LEU ASP ALA SEQRES 24 A 313 LEU ASN GLY GLY ASP SER SER GLU PRO PRO ALA ASP GLY SEQRES 25 A 313 GLY SEQRES 1 B 313 ALA GLU SER THR LEU GLY ALA ALA ALA ALA GLN SER GLY SEQRES 2 B 313 ARG TYR PHE GLY THR ALA ILE ALA SER GLY ARG LEU SER SEQRES 3 B 313 ASP SER THR TYR THR SER ILE ALA GLY ARG GLU PHE ASN SEQRES 4 B 313 MET VAL THR ALA GLU ASN GLU MET LYS ILE ASP ALA THR SEQRES 5 B 313 GLU PRO GLN ARG GLY GLN PHE ASN PHE SER SER ALA ASP SEQRES 6 B 313 ARG VAL TYR ASN TRP ALA VAL GLN ASN GLY LYS GLN VAL SEQRES 7 B 313 ARG GLY HIS THR LEU ALA TRP HIS SER GLN GLN PRO GLY SEQRES 8 B 313 TRP MET GLN SER LEU SER GLY SER ALA LEU ARG GLN ALA SEQRES 9 B 313 MET ILE ASP HIS ILE ASN GLY VAL MET ALA HIS TYR LYS SEQRES 10 B 313 GLY LYS ILE VAL GLN TRP ASP VAL VAL ASN GLU ALA PHE SEQRES 11 B 313 ALA ASP GLY SER SER GLY ALA ARG ARG ASP SER ASN LEU SEQRES 12 B 313 GLN ARG SER GLY ASN ASP TRP ILE GLU VAL ALA PHE ARG SEQRES 13 B 313 THR ALA ARG ALA ALA ASP PRO SER ALA LYS LEU CYS TYR SEQRES 14 B 313 ASN ASP TYR ASN VAL GLU ASN TRP THR TRP ALA LYS THR SEQRES 15 B 313 GLN ALA MET TYR ASN MET VAL ARG ASP PHE LYS GLN ARG SEQRES 16 B 313 GLY VAL PRO ILE ASP CYS VAL GLY PHE GLN SER HIS PHE SEQRES 17 B 313 ASN SER GLY SER PRO TYR ASN SER ASN PHE ARG THR THR SEQRES 18 B 313 LEU GLN ASN PHE ALA ALA LEU GLY VAL ASP VAL ALA ILE SEQRES 19 B 313 THR GLU LEU ASP ILE GLN GLY ALA PRO ALA SER THR TYR SEQRES 20 B 313 ALA ASN VAL THR ASN ASP CYS LEU ALA VAL SER ARG CYS SEQRES 21 B 313 LEU GLY ILE THR VAL TRP GLY VAL ARG ASP SER ASP SER SEQRES 22 B 313 TRP ARG SER GLU GLN THR PRO LEU LEU PHE ASN ASN ASP SEQRES 23 B 313 GLY SER LYS LYS ALA ALA TYR THR ALA VAL LEU ASP ALA SEQRES 24 B 313 LEU ASN GLY GLY ASP SER SER GLU PRO PRO ALA ASP GLY SEQRES 25 B 313 GLY HET X2F C 1 9 HET XYP C 2 9 HET X2F D 1 9 HET XYP D 2 9 HET GOL A 401 6 HET GOL A 402 6 HET GOL B 401 6 HETNAM X2F 2-DEOXY-2-FLUORO-ALPHA-D-XYLOPYRANOSE HETNAM XYP BETA-D-XYLOPYRANOSE HETNAM GOL GLYCEROL HETSYN X2F 2-DEOXY-2-FLUORO XYLOPYRANOSE; 2-DEOXY-2-FLUORO-ALPHA- HETSYN 2 X2F D-XYLOSE; 2-DEOXY-2-FLUORO-D-XYLOSE; 2-DEOXY-2-FLUORO- HETSYN 3 X2F XYLOSE HETSYN XYP BETA-D-XYLOSE; D-XYLOSE; XYLOSE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 X2F 2(C5 H9 F O4) FORMUL 3 XYP 2(C5 H10 O5) FORMUL 5 GOL 3(C3 H8 O3) FORMUL 8 HOH *717(H2 O) HELIX 1 AA1 THR A 4 GLN A 11 1 8 HELIX 2 AA2 ALA A 21 LEU A 25 5 5 HELIX 3 AA3 ASP A 27 PHE A 38 1 12 HELIX 4 AA4 LYS A 48 GLU A 53 1 6 HELIX 5 AA5 PHE A 61 ASN A 74 1 14 HELIX 6 AA6 PRO A 90 SER A 95 1 6 HELIX 7 AA7 SER A 97 TYR A 116 1 20 HELIX 8 AA8 SER A 141 SER A 146 1 6 HELIX 9 AA9 ASP A 149 ASP A 162 1 14 HELIX 10 AB1 TRP A 179 GLY A 196 1 18 HELIX 11 AB2 ASN A 217 ALA A 227 1 11 HELIX 12 AB3 PRO A 243 ALA A 256 1 14 HELIX 13 AB4 ARG A 269 SER A 273 5 5 HELIX 14 AB5 ARG A 275 THR A 279 5 5 HELIX 15 AB6 LYS A 290 ASN A 301 1 12 HELIX 16 AB7 THR B 4 GLN B 11 1 8 HELIX 17 AB8 ALA B 21 LEU B 25 5 5 HELIX 18 AB9 ASP B 27 PHE B 38 1 12 HELIX 19 AC1 LYS B 48 GLU B 53 1 6 HELIX 20 AC2 PHE B 61 ASN B 74 1 14 HELIX 21 AC3 PRO B 90 SER B 95 1 6 HELIX 22 AC4 SER B 97 TYR B 116 1 20 HELIX 23 AC5 SER B 141 GLY B 147 1 7 HELIX 24 AC6 ASP B 149 ASP B 162 1 14 HELIX 25 AC7 TRP B 179 GLY B 196 1 18 HELIX 26 AC8 ASN B 217 ALA B 227 1 11 HELIX 27 AC9 PRO B 243 ALA B 256 1 14 HELIX 28 AD1 ARG B 269 SER B 273 5 5 HELIX 29 AD2 ARG B 275 THR B 279 5 5 HELIX 30 AD3 LYS B 290 GLY B 302 1 13 SHEET 1 AA110 HIS A 207 PHE A 208 0 SHEET 2 AA110 ASP A 231 ILE A 239 1 O ASP A 238 N PHE A 208 SHEET 3 AA110 CYS A 260 VAL A 265 1 O LEU A 261 N VAL A 232 SHEET 4 AA110 TYR A 15 ILE A 20 1 N GLY A 17 O ILE A 263 SHEET 5 AA110 MET A 40 ALA A 43 1 O THR A 42 N ILE A 20 SHEET 6 AA110 GLN A 77 ALA A 84 1 O ARG A 79 N VAL A 41 SHEET 7 AA110 GLN A 122 ASN A 127 1 O ASP A 124 N GLY A 80 SHEET 8 AA110 LYS A 166 ASP A 171 1 O CYS A 168 N TRP A 123 SHEET 9 AA110 CYS A 201 PHE A 204 1 O GLY A 203 N TYR A 169 SHEET 10 AA110 ASP A 231 ILE A 239 1 O ALA A 233 N PHE A 204 SHEET 1 AA210 HIS B 207 PHE B 208 0 SHEET 2 AA210 ASP B 231 ILE B 239 1 O ASP B 238 N PHE B 208 SHEET 3 AA210 CYS B 260 VAL B 265 1 O LEU B 261 N VAL B 232 SHEET 4 AA210 TYR B 15 ILE B 20 1 N GLY B 17 O ILE B 263 SHEET 5 AA210 MET B 40 ALA B 43 1 O THR B 42 N ILE B 20 SHEET 6 AA210 GLN B 77 ALA B 84 1 O ARG B 79 N VAL B 41 SHEET 7 AA210 GLN B 122 ASN B 127 1 O ASP B 124 N GLY B 80 SHEET 8 AA210 LYS B 166 ASP B 171 1 O CYS B 168 N TRP B 123 SHEET 9 AA210 CYS B 201 PHE B 204 1 O GLY B 203 N TYR B 169 SHEET 10 AA210 ASP B 231 ILE B 239 1 O ALA B 233 N PHE B 204 SSBOND 1 CYS A 168 CYS A 201 1555 1555 2.06 SSBOND 2 CYS A 254 CYS A 260 1555 1555 2.05 SSBOND 3 CYS B 168 CYS B 201 1555 1555 1.99 SSBOND 4 CYS B 254 CYS B 260 1555 1555 2.06 LINK OE1 GLU A 236 C1 X2F C 1 1555 1555 1.50 LINK OE1 GLU B 236 C1 X2F D 1 1555 1555 1.50 LINK O4 X2F C 1 C1 XYP C 2 1555 1555 1.44 LINK O4 X2F D 1 C1 XYP D 2 1555 1555 1.43 CISPEP 1 HIS A 81 THR A 82 0 6.79 CISPEP 2 HIS B 81 THR B 82 0 1.84 CRYST1 49.210 81.060 72.810 90.00 102.79 90.00 P 1 21 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 0.020320 0.000000 0.004610 0.00000 SCALE2 0.000000 0.012340 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014080 0.00000 MTRIX1 1 0.999080 -0.041440 0.011400 15.98502 1 MTRIX2 1 0.042110 0.996900 -0.066520 2.67231 1 MTRIX3 1 -0.008610 0.066940 0.997720 35.57695 1