PDB Short entry for 1E5C HEADER HYDROLASE 24-JUL-00 1E5C TITLE INTERNAL XYLAN BINDING DOMAIN FROM C. FIMI XYN10A, R262G MUTANT 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; COMPND 8 MUTATION: 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 NUMMDL 5 AUTHOR P.J.SIMPSON,X.HEFANG,D.N.BOLAM,H.J.GILBERT,M.P.WILLIAMSON REVDAT 4 24-OCT-18 1E5C 1 SOURCE REVDAT 3 14-JUN-17 1E5C 1 REMARK REVDAT 2 24-FEB-09 1E5C 1 VERSN REVDAT 1 25-MAY-01 1E5C 0 JRNL AUTH P.J.SIMPSON,X.HEFANG,D.N.BOLAM,H.J.GILBERT,M.P.WILLIAMSON JRNL TITL THE STRUCTURAL BASIS FOR THE LIGAND SPECIFICITY OF FAMILY 2 JRNL TITL 2 CARBOHYDRATE BINDING NODULES JRNL REF J.BIOL.CHEM. V. 275 41137 2000 JRNL REFN ISSN 0021-9258 JRNL PMID 10973978 JRNL DOI 10.1074/JBC.M006948200 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 1E5C COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-JUL-00. REMARK 100 THE DEPOSITION ID IS D_1290005191. 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 : 50MM SODIUM PHOSPHATE, 10MM REMARK 210 AZIDE 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; 750 MHZ REMARK 210 SPECTROMETER MODEL : DRX 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 : 5 REMARK 210 CONFORMERS, SELECTION CRITERIA : 5 REPRESENTATIVE STRUCTURES REMARK 210 CHOSEN FROM 33 LOW ENERGY REMARK 210 STRUCTURES REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING HETERONUCLEAR NMR REMARK 210 SPECTROSCOPY ON A UNIFORMLY 15N-LABELLED SAMPLE OF XBD1 (R262G) 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 400 REMARK 400 COMPOUND REMARK 400 CHAIN A MUTATION: R262G 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 1 ALA A 256 -89.84 -97.68 REMARK 500 1 GLU A 258 148.85 -170.29 REMARK 500 1 SER A 260 46.05 -84.71 REMARK 500 1 ASP A 261 -36.33 -160.22 REMARK 500 1 GLN A 285 167.50 -44.26 REMARK 500 1 ALA A 293 145.66 -174.42 REMARK 500 1 SER A 298 49.39 -170.48 REMARK 500 1 MET A 318 94.93 -59.31 REMARK 500 1 SER A 322 110.42 -160.05 REMARK 500 2 THR A 254 107.06 -168.55 REMARK 500 2 ALA A 256 -90.38 -105.41 REMARK 500 2 TRP A 259 -168.83 -163.01 REMARK 500 2 SER A 260 43.33 -84.34 REMARK 500 2 ASP A 261 -38.03 -155.68 REMARK 500 2 ALA A 293 148.29 -175.74 REMARK 500 2 SER A 298 58.59 -170.54 REMARK 500 2 SER A 309 11.48 -140.35 REMARK 500 2 MET A 318 108.44 -59.56 REMARK 500 2 SER A 322 102.53 -161.16 REMARK 500 3 CYS A 249 171.32 -59.69 REMARK 500 3 THR A 254 112.17 -164.68 REMARK 500 3 ALA A 256 -92.94 -100.63 REMARK 500 3 TRP A 259 -169.27 -161.21 REMARK 500 3 SER A 260 44.56 -84.13 REMARK 500 3 ASP A 261 -35.50 -159.57 REMARK 500 3 GLN A 285 173.37 -46.99 REMARK 500 3 ALA A 293 148.37 -178.07 REMARK 500 3 SER A 298 48.23 -170.39 REMARK 500 3 SER A 309 18.55 -150.72 REMARK 500 3 SER A 322 99.99 -160.15 REMARK 500 4 THR A 254 115.12 -169.02 REMARK 500 4 ALA A 256 -89.50 -101.86 REMARK 500 4 GLU A 258 149.30 -170.41 REMARK 500 4 SER A 260 47.11 -86.50 REMARK 500 4 ASP A 261 -37.22 -160.23 REMARK 500 4 GLN A 285 166.96 -43.88 REMARK 500 4 ALA A 293 149.20 -178.34 REMARK 500 4 SER A 298 79.44 -170.45 REMARK 500 4 SER A 300 -54.83 -153.27 REMARK 500 4 SER A 309 27.01 -165.59 REMARK 500 4 THR A 324 129.14 -36.09 REMARK 500 5 CYS A 249 172.07 -59.72 REMARK 500 5 THR A 254 104.46 -167.08 REMARK 500 5 ALA A 256 -83.08 -103.58 REMARK 500 5 GLU A 258 146.62 -170.41 REMARK 500 5 SER A 260 45.65 -84.19 REMARK 500 5 ASP A 261 -36.84 -159.99 REMARK 500 5 GLN A 285 171.03 -45.33 REMARK 500 5 SER A 298 133.97 -170.40 REMARK 500 5 SER A 300 -51.08 -162.49 REMARK 500 REMARK 500 THIS ENTRY HAS 54 RAMACHANDRAN OUTLIERS. 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 1 ARG A 255 0.32 SIDE CHAIN REMARK 500 1 ARG A 302 0.29 SIDE CHAIN REMARK 500 2 ARG A 255 0.27 SIDE CHAIN REMARK 500 3 ARG A 255 0.21 SIDE CHAIN REMARK 500 3 ARG A 302 0.10 SIDE CHAIN REMARK 500 4 ARG A 255 0.21 SIDE CHAIN REMARK 500 5 ARG A 255 0.31 SIDE CHAIN REMARK 500 5 ARG A 302 0.32 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2XBD RELATED DB: PDB REMARK 900 INTERNAL XYLAN BINDING DOMAIN FROM CELLULOMONAS FIMI XYLANASE D, REMARK 900 NMR, MINIMIZED AVERAGE STRUCTURE REMARK 900 RELATED ID: 1XBD RELATED DB: PDB REMARK 900 INTERNAL XYLAN BINDING DOMAIN FROM CELLULOMONAS FIMI XYLANASE D, REMARK 900 NMR, 5 STRUCTURES REMARK 900 RELATED ID: 1E5B RELATED DB: PDB REMARK 900 INTERNAL XYLAN BINDING DOMAIN FROM C. FIMI XYN10A, R262G MUTANT REMARK 900 RELATED ID: 4623 RELATED DB: BMRB DBREF 1E5C A 247 333 UNP P54865 XYND_CELFI 247 333 SEQADV 1E5C GLY A 262 UNP P54865 ARG 262 ENGINEERED MUTATION SEQRES 1 A 87 THR GLY CYS SER VAL THR ALA THR ARG ALA GLU GLU TRP SEQRES 2 A 87 SER ASP GLY 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 CYS A 249 TRP A 259 0 SHEET 2 A 4 GLY A 262 VAL A 269 -1 N THR A 266 O THR A 254 SHEET 3 A 4 ASN A 311 MET A 318 -1 O PHE A 313 N TYR A 267 SHEET 4 A 4 THR A 286 TRP A 291 -1 N GLN A 288 O THR A 316 SHEET 1 B 4 ASN A 294 GLY A 297 0 SHEET 2 B 4 THR A 301 PRO A 306 -1 O THR A 303 N THR A 296 SHEET 3 B 4 TRP A 275 LEU A 281 -1 O LEU A 279 N ARG A 302 SHEET 4 B 4 PRO A 326 CYS A 330 -1 O ALA A 327 N ALA A 280 SSBOND 1 CYS A 249 CYS A 330 1555 1555 2.02 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