HEADER SUGAR BINDING PROTEIN 27-JUN-18 6A6C TITLE CRYSTAL STRUCTURE OF CARBOHYDRATE-BINDING MODULE FAMILY 56 BETA-1,3- TITLE 2 GLUCAN BINDING DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-1,3-GLUCANASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.1.39; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: SF FILE CONTAINS FRIEDEL PAIRS. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PAENIBACILLUS BARENGOLTZII; SOURCE 3 ORGANISM_TAXID: 343517; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS CARBOHYDRATE-BINDING MODULE FAMILY 56, BETA-1, 3-GLUCAN, SUGAR KEYWDS 2 BINDING, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Z.QIN,S.LIN REVDAT 2 22-NOV-23 6A6C 1 REMARK REVDAT 1 03-JUL-19 6A6C 0 JRNL AUTH Z.QIN,S.LIN JRNL TITL CRYSTAL STRUCTURE OF CARBOHYDRATE-BINDING MODULE FAMILY 56 JRNL TITL 2 BETA-1,3-GLUCAN BINDING DOMAIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.47 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 87.7 REMARK 3 NUMBER OF REFLECTIONS : 8208 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 809 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 9.4738 - 4.0931 0.95 1121 130 0.1801 0.2023 REMARK 3 2 4.0931 - 3.2502 0.98 1150 126 0.2057 0.2869 REMARK 3 3 3.2502 - 2.8397 0.98 1153 126 0.2365 0.3416 REMARK 3 4 2.8397 - 2.0800 0.92 1081 119 0.2514 0.3418 REMARK 3 5 2.0800 - 2.0500 0.00 0 0 0.0000 0.0000 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.370 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.970 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 687 REMARK 3 ANGLE : 0.928 935 REMARK 3 CHIRALITY : 0.067 102 REMARK 3 PLANARITY : 0.005 120 REMARK 3 DIHEDRAL : 4.407 383 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6A6C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1300008225. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-OCT-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0093 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8208 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 33.712 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 87.7 REMARK 200 DATA REDUNDANCY : 18.50 REMARK 200 R MERGE (I) : 0.10500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.8600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.41200 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: PHENIX REMARK 200 STARTING MODEL: 5H9X REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 14 MM SODIUM CHOLATE,1.4 M DI-AMMONIUM REMARK 280 TARTRATE, 20 DAYS, PH 7.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 11555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 12555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 13555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 14555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 15555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 16555 -Y+1/2,-X+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 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 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 33.71200 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 33.71200 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 37.49400 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 33.71200 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 33.71200 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 37.49400 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 33.71200 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 33.71200 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 37.49400 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 33.71200 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 33.71200 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 37.49400 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 33.71200 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 33.71200 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 37.49400 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 33.71200 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 33.71200 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 37.49400 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 33.71200 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 33.71200 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 37.49400 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 33.71200 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 33.71200 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 37.49400 REMARK 290 REMARK 290 REMARK: NULL 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 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 VAL A 74 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 VAL A 22 -167.51 -116.35 REMARK 500 THR A 80 172.47 -58.54 REMARK 500 REMARK 500 REMARK: NULL DBREF1 6A6C A 1 85 UNP A0A1S4NYE1_9BACL DBREF2 6A6C A A0A1S4NYE1 4 88 SEQRES 1 A 85 ALA ASP PHE THR GLN GLY ALA ASP VAL SER GLY ASN ASN SEQRES 2 A 85 VAL THR LEU TRP PHE LYS SER SER VAL ASN THR THR TRP SEQRES 3 A 85 VAL ASP VAL HIS TYR LYS VAL ASN SER GLY VAL GLN GLN SEQRES 4 A 85 ASN VAL ARG MET SER PHE ASN ALA GLY ALA ALA ARG PHE SEQRES 5 A 85 GLU HIS THR ILE LEU THR ALA ALA GLN ALA GLU ILE GLU SEQRES 6 A 85 TYR PHE PHE THR TYR ASN ASN GLY VAL PRO ALA TYR ASP SEQRES 7 A 85 THR THR THR PHE THR TYR ARG FORMUL 2 HOH *2(H2 O) SHEET 1 AA1 4 PHE A 3 SER A 10 0 SHEET 2 AA1 4 ASN A 13 SER A 20 -1 O LYS A 19 N THR A 4 SHEET 3 AA1 4 ARG A 51 ILE A 56 -1 O ILE A 56 N VAL A 14 SHEET 4 AA1 4 SER A 44 ASN A 46 -1 N ASN A 46 O ARG A 51 SHEET 1 AA2 4 GLN A 39 ARG A 42 0 SHEET 2 AA2 4 VAL A 27 VAL A 33 -1 N TYR A 31 O GLN A 39 SHEET 3 AA2 4 ILE A 64 ASN A 71 -1 O GLU A 65 N LYS A 32 SHEET 4 AA2 4 ALA A 76 ASP A 78 -1 O TYR A 77 N TYR A 70 SHEET 1 AA3 4 GLN A 39 ARG A 42 0 SHEET 2 AA3 4 VAL A 27 VAL A 33 -1 N TYR A 31 O GLN A 39 SHEET 3 AA3 4 ILE A 64 ASN A 71 -1 O GLU A 65 N LYS A 32 SHEET 4 AA3 4 PHE A 82 TYR A 84 -1 O PHE A 82 N TYR A 66 CRYST1 67.424 67.424 74.988 90.00 90.00 90.00 I 4 2 2 16 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 0.014832 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014832 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013335 0.00000