PDB Short entry for 2XBD HEADER HYDROLASE 27-OCT-98 2XBD TITLE INTERNAL XYLAN BINDING DOMAIN FROM CELLULOMONAS FIMI XYLANASE D, NMR, TITLE 2 MINIMIZED AVERAGE STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: XYLANASE D; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: XYLAN BINDING DOMAIN 1; COMPND 5 SYNONYM: XBD1, ENDO-1,4-BETA-XYLANASE D; COMPND 6 EC: 3.2.1.8; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CELLULOMONAS FIMI; SOURCE 3 ORGANISM_TAXID: 1708; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: JM83 KEYWDS HYDROLASE, XYLAN BINDING DOMAIN, XYLANASE, BETA-SHEET EXPDTA SOLUTION NMR AUTHOR P.J.SIMPSON,D.N.BOLAM,A.COOPER,A.CIRUELA,G.P.HAZLEWOOD,H.J.GILBERT, AUTHOR 2 M.P.WILLIAMSON REVDAT 3 16-MAR-22 2XBD 1 REMARK REVDAT 2 24-FEB-09 2XBD 1 VERSN REVDAT 1 21-JUL-99 2XBD 0 JRNL AUTH P.J.SIMPSON,D.N.BOLAM,A.COOPER,A.CIRUELA,G.P.HAZLEWOOD, JRNL AUTH 2 H.J.GILBERT,M.P.WILLIAMSON JRNL TITL A FAMILY IIB XYLAN-BINDING DOMAIN HAS A SIMILAR SECONDARY JRNL TITL 2 STRUCTURE TO A HOMOLOGOUS FAMILY IIA CELLULOSE-BINDING JRNL TITL 3 DOMAIN BUT DIFFERENT LIGAND SPECIFICITY. JRNL REF STRUCTURE FOLD.DES. V. 7 853 1999 JRNL REFN ISSN 0969-2126 JRNL PMID 10425686 JRNL DOI 10.1016/S0969-2126(99)80108-7 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: YASAP REMARK 4 REMARK 4 2XBD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000178754. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310 REMARK 210 PH : 5.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : TOCSY; DQF-COSY; NOESY; E.COSY; REMARK 210 HSQC; NOESY-HMQC; TOCSY-HMQC; REMARK 210 HNHA; HNHB REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : DRX500; DRX600; DRX800 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : MSI FELIX 97.0 REMARK 210 METHOD USED : HYBRID DISTANCE GEOMETRY/ REMARK 210 SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : MINIMIZED AVERAGE STRUCTURE, REMARK 210 CALCULATED FROM 38 LOWEST ENERGY REMARK 210 STRUCTURES REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING HETERONUCLEAR NMR REMARK 210 SPECTROSCOPY ON A UNIFORMLY 15N-LABELLED SAMPLE OF XBD1 REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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 256 -80.56 -92.05 REMARK 500 ARG A 262 170.15 174.80 REMARK 500 ALA A 293 149.94 177.79 REMARK 500 LYS A 319 -73.88 -60.30 REMARK 500 THR A 325 159.68 -47.03 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 255 0.23 SIDE CHAIN REMARK 500 ARG A 262 0.32 SIDE CHAIN REMARK 500 ARG A 302 0.31 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: XBD REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: BINDING SITE TRYPTOPHANS DBREF 2XBD A 247 333 UNP P54865 XYND_CELFI 247 333 SEQRES 1 A 87 THR GLY CYS SER VAL THR ALA THR ARG ALA GLU GLU TRP SEQRES 2 A 87 SER ASP ARG PHE ASN VAL THR TYR SER VAL SER GLY SER SEQRES 3 A 87 SER ALA TRP THR VAL ASN LEU ALA LEU ASN GLY SER GLN SEQRES 4 A 87 THR ILE GLN ALA SER TRP ASN ALA ASN VAL THR GLY SER SEQRES 5 A 87 GLY SER THR ARG THR VAL THR PRO ASN GLY SER GLY ASN SEQRES 6 A 87 THR PHE GLY VAL THR VAL MET LYS ASN GLY SER SER THR SEQRES 7 A 87 THR PRO ALA ALA THR CYS ALA GLY SER SHEET 1 A 4 THR A 252 ARG A 255 0 SHEET 2 A 4 ARG A 262 SER A 268 -1 N SER A 268 O THR A 252 SHEET 3 A 4 THR A 312 MET A 318 -1 N VAL A 317 O PHE A 263 SHEET 4 A 4 ILE A 287 TRP A 291 -1 N TRP A 291 O GLY A 314 SHEET 1 B 4 ALA A 328 CYS A 330 0 SHEET 2 B 4 VAL A 277 LEU A 279 -1 N ASN A 278 O THR A 329 SHEET 3 B 4 ARG A 302 THR A 305 -1 N VAL A 304 O VAL A 277 SHEET 4 B 4 ASN A 294 THR A 296 -1 N THR A 296 O THR A 303 SSBOND 1 CYS A 249 CYS A 330 1555 1555 2.02 SITE 1 XBD 2 TRP A 259 TRP A 291 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000