HEADER HYDROLASE 19-DEC-01 1KNN OBSLTE 11-SEP-02 1KNN 1MC9 TITLE STREPROMYCES LIVIDANS XYLAN BINDING DOMAIN CBM13 IN COMPLEX TITLE 2 WITH XYLOPENTAOSE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDO-1,4-BETA-XYLANASE A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CARBOHYDRATE BINDING MODULE (RESIDUES 348-477); COMPND 5 SYNONYM: XYLANASE A, 1,4-BETA-D-XYLAN XYLANOHYDROLASE A; COMPND 6 EC: 3.2.1.8; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES LIVIDANS; SOURCE 3 ORGANISM_COMMON: BACTERIA; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_COMMON: BACTERIA KEYWDS XYLANASE A XYLAN BINDING DOMAIN CBM13, LECTIN-LIKE BETA- KEYWDS 2 TREFOIL FOLD, XYLOPENTAOSE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR V.NOTENBOOM,A.B.BORASTON,S.J.WILLIAMS,D.G.KILBURN,D.R.ROSE REVDAT 2 11-SEP-02 1KNN 1 OBSLTE REVDAT 1 19-JUN-02 1KNN 0 JRNL AUTH V.NOTENBOOM,A.B.BORASTON,S.J.WILLIAMS,D.G.KILBURN, JRNL AUTH 2 D.R.ROSE JRNL TITL HIGH-RESOLUTION CRYSTAL STRUCTURES OF THE JRNL TITL 2 LECTIN-LIKE XYLAN BINDING DOMAIN FROM STREPROMYCES JRNL TITL 3 LIVIDANS XYLANASE 10A WITH BOUND SUBSTRATES REVEAL JRNL TITL 4 A NOVEL MODE OF XYLAN BINDING JRNL REF BIOCHEMISTRY V. 41 4246 2002 JRNL REFN ASTM BICHAW US ISSN 0006-2960 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.05 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 13471 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 664 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 924 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 51 REMARK 3 SOLVENT ATOMS : 193 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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) : 0.007 ; NULL REMARK 3 ANGLE DISTANCE (A) : 1.440 ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL 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) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL 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 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1KNN COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-JAN-2002. REMARK 100 THE RCSB ID CODE IS RCSB015149. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAR-2000 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 14-BM-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL 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 : 13471 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 18.050 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 83.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 23.4 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: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8 MM AMMONIUM SULFATE, 50 MM MES REMARK 280 PH 6.5, 5% DIOXANE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 300K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,2/3+Z REMARK 290 3555 -X+Y,-X,1/3+Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,1/3-Z REMARK 290 6555 -X,-X+Y,2/3-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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.42800 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 26.71400 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 26.71400 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 53.42800 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). 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 APPLY THE FOLLOWING TO CHAINS: A, B 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH 296 LIES ON A SPECIAL POSITION. 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 GLU A 0 REMARK 465 PRO A 1 REMARK 465 PRO A 2 REMARK 465 ALA A 3 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 REMARK 500 O HOH 155 O HOH 315 2.04 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),F6.3) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 LEU A 85 CG LEU A 85 CD1 1.114 REMARK 500 LEU A 85 CG LEU A 85 CD2 0.594 REMARK 500 LEU A 85 CA LEU A 85 C 0.449 REMARK 500 ASN A 86 CG ASN A 86 OD1 1.312 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: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LEU A 30 CA - CB - CG ANGL. DEV. =-15.2 DEGREES REMARK 500 LEU A 85 CB - CG - CD1 ANGL. DEV. =-22.8 DEGREES REMARK 500 LEU A 85 N - CA - C ANGL. DEV. =-18.6 DEGREES REMARK 500 ASN A 86 OD1 - CG - ND2 ANGL. DEV. =-19.7 DEGREES REMARK 500 ASN A 86 CB - CG - OD1 ANGL. DEV. =-39.4 DEGREES REMARK 500 ASN A 86 N - CA - C ANGL. DEV. =-18.5 DEGREES 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 M RES CSSEQI PSI PHI REMARK 500 ARG A 128 -173.71 92.02 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1KNL RELATED DB: PDB REMARK 900 STREPROMYCES LIVIDANS XYLAN BINDING DOMAIN CBM13 REMARK 900 RELATED ID: 1KNM RELATED DB: PDB REMARK 900 STREPROMYCES LIVIDANS XYLAN BINDING DOMAIN CBM13 IN COMPLEX REMARK 900 WITH LACTOSE DBREF 1KNN A 0 129 UNP P26514 XYNA_STRLI 348 477 SEQRES 1 A 130 GLU PRO PRO ALA ASP GLY GLY GLN ILE LYS GLY VAL GLY SEQRES 2 A 130 SER GLY ARG CYS LEU ASP VAL PRO ASP ALA SER THR SER SEQRES 3 A 130 ASP GLY THR GLN LEU GLN LEU TRP ASP CYS HIS SER GLY SEQRES 4 A 130 THR ASN GLN GLN TRP ALA ALA THR ASP ALA GLY GLU LEU SEQRES 5 A 130 ARG VAL TYR GLY ASP LYS CYS LEU ASP ALA ALA GLY THR SEQRES 6 A 130 SER ASN GLY SER LYS VAL GLN ILE TYR SER CYS TRP GLY SEQRES 7 A 130 GLY ASP ASN GLN LYS TRP ARG LEU ASN SER ASP GLY SER SEQRES 8 A 130 VAL VAL GLY VAL GLN SER GLY LEU CYS LEU ASP ALA VAL SEQRES 9 A 130 GLY ASN GLY THR ALA ASN GLY THR LEU ILE GLN LEU TYR SEQRES 10 A 130 THR CYS SER ASN GLY SER ASN GLN ARG TRP THR ARG THR HET XYS B 131 10 HET XYS B 132 9 HET XYS B 133 9 HET XYS B 134 9 HET XYS B 135 9 HET SO4 130 5 HET GOL 136 6 HETNAM XYS XYLOPYRANOSE HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL FORMUL 2 XYS 5(C5 H10 O5) FORMUL 6 SO4 O4 S 2- FORMUL 7 GOL C3 H8 O3 FORMUL 8 HOH *187(H2 O1) HELIX 1 1 VAL A 19 SER A 23 5 5 HELIX 2 2 GLY A 38 GLN A 42 5 5 HELIX 3 3 GLY A 78 GLN A 81 5 4 HELIX 4 4 GLY A 104 GLY A 106 5 3 HELIX 5 5 GLY A 121 GLN A 124 5 4 SHEET 1 A 2 LYS A 9 GLY A 10 0 SHEET 2 A 2 TRP A 126 THR A 127 -1 O THR A 127 N LYS A 9 SHEET 1 B 2 CYS A 16 ASP A 18 0 SHEET 2 B 2 GLN A 31 TRP A 33 -1 O GLN A 31 N ASP A 18 SHEET 1 C 4 ALA A 44 ALA A 45 0 SHEET 2 C 4 LEU A 51 VAL A 53 -1 O ARG A 52 N ALA A 44 SHEET 3 C 4 LYS A 57 ALA A 61 -1 O LYS A 57 N VAL A 53 SHEET 4 C 4 VAL A 70 SER A 74 -1 O TYR A 73 N CYS A 58 SHEET 1 D 2 TRP A 83 LEU A 85 0 SHEET 2 D 2 VAL A 91 GLY A 93 -1 O VAL A 92 N ARG A 84 SHEET 1 E 2 CYS A 99 ALA A 102 0 SHEET 2 E 2 ILE A 113 TYR A 116 -1 O TYR A 116 N CYS A 99 SSBOND 1 CYS A 16 CYS A 35 SSBOND 2 CYS A 58 CYS A 75 SSBOND 3 CYS A 99 CYS A 118 LINK O4 XYS B 131 C1 XYS B 132 LINK O4 XYS B 132 C1 XYS B 133 LINK O4 XYS B 133 C1 XYS B 134 LINK O4 XYS B 134 C1 XYS B 135 CRYST1 55.130 55.130 80.142 90.00 90.00 120.00 P 32 2 1 6 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 0.018139 0.010473 0.000000 0.00000 SCALE2 0.000000 0.020945 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012478 0.00000