HEADER HYDROLASE 05-OCT-01 1K42 TITLE THE SOLUTION STRUCTURE OF THE CBM4-2 CARBOHYDRATE BINDING MODULE FROM TITLE 2 A THERMOSTABLE RHODOTHERMUS MARINUS XYLANASE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: XYLANASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SECOND FAMILY 4 CARBOHYDRATE BINDING MODULE (CBM4-2) COMPND 5 (RESIDUES 211-373); COMPND 6 EC: 3.2.1.8; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHODOTHERMUS MARINUS; SOURCE 3 ORGANISM_TAXID: 29549; SOURCE 4 GENE: XYN10A; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-25B(+) KEYWDS BETA-SANDWICH FORMED BY 11 STRANDS. BINDING-SITE CLEFT. SOLVENT KEYWDS 2 EXPOSED AROMATICS (TRP69, PHE110) IN BINDING CLEFT. TWO HELICAL KEYWDS 3 TWISTS. TWO CALCIUM BINDING SITES., HYDROLASE EXPDTA SOLUTION NMR NUMMDL 12 AUTHOR P.J.SIMPSON,S.J.JAMIESON,M.ABOU-HACHEM,E.NORDBERG-KARLSSON, AUTHOR 2 H.J.GILBERT,O.HOLST,M.P.WILLIAMSON REVDAT 5 22-MAY-24 1K42 1 REMARK REVDAT 4 23-FEB-22 1K42 1 REMARK SEQADV REVDAT 3 24-FEB-09 1K42 1 VERSN REVDAT 2 01-APR-03 1K42 1 JRNL REVDAT 1 29-MAY-02 1K42 0 JRNL AUTH P.J.SIMPSON,S.J.JAMIESON,M.ABOU-HACHEM,E.N.KARLSSON, JRNL AUTH 2 H.J.GILBERT,O.HOLST,M.P.WILLIAMSON JRNL TITL THE SOLUTION STRUCTURE OF THE CBM4-2 CARBOHYDRATE BINDING JRNL TITL 2 MODULE FROM A THERMOSTABLE RHODOTHERMUS MARINUS XYLANASE. JRNL REF BIOCHEMISTRY V. 41 5712 2002 JRNL REFN ISSN 0006-2960 JRNL PMID 11980475 JRNL DOI 10.1021/BI012093I REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : FELIX 2000, X-PLOR 3.1 REMARK 3 AUTHORS : MOLECULAR SIMULATIONS INC. (FELIX), AXEL T. REMARK 3 BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE FINAL SET OF RESTRAINTS CONTAINED REMARK 3 1654 NON-REDUNDANT UNAMBIGUOUS NOES AND 17 AMBIGUOUS NOES, 93 REMARK 3 DIHEDRAL ANGLE RESTRAINTS, 72 CHI1 AND 1 CHI2 RESTRAINT, AND 65 REMARK 3 PAIRS OF HYDROGEN BOND RESTRAINTS, PLUS 177 BACKBONE DIHEDRAL REMARK 3 RESTRAINTS BASED ON 13C SHIFTS FROM TALOS. REMARK 4 REMARK 4 1K42 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-OCT-01. REMARK 100 THE DEPOSITION ID IS D_1000014534. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 0.2 M REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.5 MM CBM4-2 15N-LABELLED, AND REMARK 210 13C,15N DOUBLE LABELLED PROTEIN; REMARK 210 50 MM CACL2, 50 MM SODIUM REMARK 210 ACETATE-D3, PH 6.0, 10% D2O, 10 REMARK 210 MM SODIUM AZIDE, 0.1 MM SODIUM REMARK 210 TRIMETHYLSILYLPROPIONATE (TSP) REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY; HNHA REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR 3.1 REMARK 210 METHOD USED : HYBRID DISTANCE REMARK 210 GEOMETRY/SIMULATED ANNEALING REMARK 210 USING XPLOR REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 12 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY,STRUCTURES REMARK 210 WITH THE LEAST RESTRAINT REMARK 210 VIOLATIONS,STRUCTURES WITH THE REMARK 210 LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: NULL 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 1 LEU A 2 101.30 -57.09 REMARK 500 1 ALA A 15 155.51 -40.02 REMARK 500 1 VAL A 36 87.86 -64.64 REMARK 500 1 ASN A 54 37.77 -160.02 REMARK 500 1 ASN A 62 56.41 -149.51 REMARK 500 1 PRO A 68 38.88 -79.52 REMARK 500 1 TRP A 69 50.05 -162.58 REMARK 500 1 ARG A 93 119.12 -164.40 REMARK 500 1 ARG A 115 119.46 -178.78 REMARK 500 1 GLU A 118 66.32 79.42 REMARK 500 1 GLU A 124 -168.78 -106.65 REMARK 500 1 PHE A 130 -172.69 -173.22 REMARK 500 1 ASP A 136 -91.74 -102.91 REMARK 500 1 GLN A 137 50.59 -162.27 REMARK 500 1 ASP A 160 136.41 -173.89 REMARK 500 1 LEU A 162 94.04 -60.01 REMARK 500 2 VAL A 3 -169.71 43.85 REMARK 500 2 ALA A 15 165.48 -42.05 REMARK 500 2 VAL A 36 94.53 -46.18 REMARK 500 2 ASN A 54 22.85 -152.74 REMARK 500 2 ASN A 62 58.55 -154.40 REMARK 500 2 PHE A 76 162.86 179.53 REMARK 500 2 ARG A 93 118.49 -164.14 REMARK 500 2 GLN A 108 3.81 -68.34 REMARK 500 2 TYR A 113 -70.74 -96.17 REMARK 500 2 GLU A 118 58.56 77.28 REMARK 500 2 GLU A 124 -168.87 -108.42 REMARK 500 2 PHE A 130 -177.64 -171.89 REMARK 500 2 ASP A 136 -90.87 -106.74 REMARK 500 2 GLN A 137 53.97 -163.98 REMARK 500 2 ASP A 160 136.34 -173.80 REMARK 500 3 ALA A 15 163.53 -41.59 REMARK 500 3 VAL A 36 89.46 -67.68 REMARK 500 3 PRO A 40 -165.74 -77.46 REMARK 500 3 ALA A 50 155.18 -44.31 REMARK 500 3 ASN A 54 35.64 -156.63 REMARK 500 3 ASN A 62 60.34 -160.11 REMARK 500 3 PHE A 76 160.44 179.44 REMARK 500 3 TYR A 113 -69.88 -102.78 REMARK 500 3 ARG A 115 109.65 -164.42 REMARK 500 3 GLU A 118 68.74 79.33 REMARK 500 3 GLU A 124 -169.00 -107.67 REMARK 500 3 PHE A 130 -172.61 -173.41 REMARK 500 3 GLN A 137 27.28 86.97 REMARK 500 3 ASP A 160 136.01 -173.82 REMARK 500 3 LEU A 162 91.29 -59.43 REMARK 500 4 ALA A 15 166.00 -42.11 REMARK 500 4 VAL A 36 88.55 -67.35 REMARK 500 4 PRO A 40 -169.93 -77.44 REMARK 500 4 ASN A 54 38.62 -160.09 REMARK 500 REMARK 500 THIS ENTRY HAS 178 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 81 0.29 SIDE CHAIN REMARK 500 1 ARG A 93 0.23 SIDE CHAIN REMARK 500 1 ARG A 115 0.32 SIDE CHAIN REMARK 500 2 ARG A 81 0.19 SIDE CHAIN REMARK 500 2 ARG A 93 0.20 SIDE CHAIN REMARK 500 2 ARG A 115 0.31 SIDE CHAIN REMARK 500 2 ARG A 142 0.19 SIDE CHAIN REMARK 500 3 ARG A 81 0.32 SIDE CHAIN REMARK 500 3 ARG A 93 0.28 SIDE CHAIN REMARK 500 3 ARG A 115 0.23 SIDE CHAIN REMARK 500 3 ARG A 142 0.24 SIDE CHAIN REMARK 500 4 ARG A 81 0.32 SIDE CHAIN REMARK 500 4 ARG A 93 0.22 SIDE CHAIN REMARK 500 4 ARG A 115 0.25 SIDE CHAIN REMARK 500 4 ARG A 142 0.19 SIDE CHAIN REMARK 500 5 ARG A 81 0.28 SIDE CHAIN REMARK 500 5 ARG A 93 0.12 SIDE CHAIN REMARK 500 5 ARG A 115 0.31 SIDE CHAIN REMARK 500 5 ARG A 142 0.14 SIDE CHAIN REMARK 500 6 ARG A 81 0.23 SIDE CHAIN REMARK 500 6 ARG A 93 0.17 SIDE CHAIN REMARK 500 6 ARG A 115 0.15 SIDE CHAIN REMARK 500 6 ARG A 142 0.29 SIDE CHAIN REMARK 500 7 ARG A 81 0.19 SIDE CHAIN REMARK 500 7 ARG A 93 0.18 SIDE CHAIN REMARK 500 7 ARG A 115 0.28 SIDE CHAIN REMARK 500 7 ARG A 142 0.26 SIDE CHAIN REMARK 500 8 ARG A 81 0.18 SIDE CHAIN REMARK 500 8 ARG A 93 0.30 SIDE CHAIN REMARK 500 8 ARG A 115 0.26 SIDE CHAIN REMARK 500 8 ARG A 142 0.22 SIDE CHAIN REMARK 500 9 ARG A 81 0.31 SIDE CHAIN REMARK 500 9 ARG A 93 0.12 SIDE CHAIN REMARK 500 9 ARG A 115 0.31 SIDE CHAIN REMARK 500 9 ARG A 142 0.18 SIDE CHAIN REMARK 500 10 ARG A 81 0.32 SIDE CHAIN REMARK 500 10 ARG A 93 0.32 SIDE CHAIN REMARK 500 10 ARG A 115 0.30 SIDE CHAIN REMARK 500 10 ARG A 142 0.24 SIDE CHAIN REMARK 500 11 ARG A 81 0.24 SIDE CHAIN REMARK 500 11 ARG A 93 0.15 SIDE CHAIN REMARK 500 11 ARG A 115 0.26 SIDE CHAIN REMARK 500 11 ARG A 142 0.24 SIDE CHAIN REMARK 500 12 ARG A 81 0.22 SIDE CHAIN REMARK 500 12 ARG A 93 0.14 SIDE CHAIN REMARK 500 12 ARG A 115 0.24 SIDE CHAIN REMARK 500 12 ARG A 142 0.31 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1K45 RELATED DB: PDB REMARK 900 1K45 CONTAINS THE MINIMIZED AVERAGE STRUCTURE FOR THIS PROTEIN DBREF 1K42 A 2 164 UNP P96988 P96988_RHOMR 211 373 SEQADV 1K42 MET A 1 UNP P96988 INITIATING METHIONINE SEQADV 1K42 ALA A 165 UNP P96988 CLONING ARTIFACT SEQADV 1K42 SER A 166 UNP P96988 CLONING ARTIFACT SEQADV 1K42 GLN A 167 UNP P96988 CLONING ARTIFACT SEQADV 1K42 PRO A 168 UNP P96988 CLONING ARTIFACT SEQRES 1 A 168 MET LEU VAL ALA ASN ILE ASN GLY GLY PHE GLU SER THR SEQRES 2 A 168 PRO ALA GLY VAL VAL THR ASP LEU ALA GLU GLY VAL GLU SEQRES 3 A 168 GLY TRP ASP LEU ASN VAL GLY SER SER VAL THR ASN PRO SEQRES 4 A 168 PRO VAL PHE GLU VAL LEU GLU THR SER ASP ALA PRO GLU SEQRES 5 A 168 GLY ASN LYS VAL LEU ALA VAL THR VAL ASN GLY VAL GLY SEQRES 6 A 168 ASN ASN PRO TRP ASP ILE GLU ALA THR ALA PHE PRO VAL SEQRES 7 A 168 ASN VAL ARG PRO GLY VAL THR TYR THR TYR THR ILE TRP SEQRES 8 A 168 ALA ARG ALA GLU GLN ASP GLY ALA VAL VAL SER PHE THR SEQRES 9 A 168 VAL GLY ASN GLN SER PHE GLN GLU TYR GLY ARG LEU HIS SEQRES 10 A 168 GLU GLN GLN ILE THR THR GLU TRP GLN PRO PHE THR PHE SEQRES 11 A 168 GLU PHE THR VAL SER ASP GLN GLU THR VAL ILE ARG ALA SEQRES 12 A 168 PRO ILE HIS PHE GLY TYR ALA ALA ASN VAL GLY ASN THR SEQRES 13 A 168 ILE TYR ILE ASP GLY LEU ALA ILE ALA SER GLN PRO HELIX 1 1 ASP A 20 GLY A 24 5 5 HELIX 2 2 TYR A 149 VAL A 153 5 5 SHEET 1 A 6 GLY A 16 VAL A 17 0 SHEET 2 A 6 VAL A 41 GLU A 46 -1 O VAL A 44 N GLY A 16 SHEET 3 A 6 LYS A 55 VAL A 61 -1 O VAL A 56 N LEU A 45 SHEET 4 A 6 ASN A 155 ALA A 165 -1 O ILE A 159 N LEU A 57 SHEET 5 A 6 THR A 85 ALA A 94 -1 N THR A 89 O ALA A 163 SHEET 6 A 6 GLN A 126 THR A 133 -1 O PHE A 128 N ILE A 90 SHEET 1 B 5 TRP A 28 VAL A 32 0 SHEET 2 B 5 ILE A 71 ASN A 79 -1 O THR A 74 N ASP A 29 SHEET 3 B 5 VAL A 140 PHE A 147 -1 O ILE A 145 N ALA A 73 SHEET 4 B 5 ALA A 99 GLY A 106 -1 N GLY A 106 O ARG A 142 SHEET 5 B 5 GLU A 112 ILE A 121 -1 O GLN A 119 N VAL A 101 CISPEP 1 PHE A 76 PRO A 77 1 -0.75 CISPEP 2 PHE A 76 PRO A 77 2 -0.53 CISPEP 3 PHE A 76 PRO A 77 3 -0.50 CISPEP 4 PHE A 76 PRO A 77 4 -0.84 CISPEP 5 PHE A 76 PRO A 77 5 -0.68 CISPEP 6 PHE A 76 PRO A 77 6 -0.24 CISPEP 7 PHE A 76 PRO A 77 7 -0.15 CISPEP 8 PHE A 76 PRO A 77 8 -0.57 CISPEP 9 PHE A 76 PRO A 77 9 -0.36 CISPEP 10 PHE A 76 PRO A 77 10 -0.47 CISPEP 11 PHE A 76 PRO A 77 11 -0.36 CISPEP 12 PHE A 76 PRO A 77 12 -0.65 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 MODEL 1