HEADER HYDROLASE 03-OCT-19 6UJF TITLE CRYSTAL STRUCTURE OF THE CLOSTRIDIAL CELLULOSE SYNTHASE SUBUNIT Z TITLE 2 (CCSZ) FROM CLOSTRIDIOIDES DIFFICILE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDOGLUCANASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.1.4; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CLOSTRIDIOIDES DIFFICILE; SOURCE 3 ORGANISM_TAXID: 1496; SOURCE 4 GENE: CELH, SAMEA1402348_00819; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: CODONPLUS KEYWDS GLYCOSYL, HYDROLASE, BIOFILM, CELLULOSE, GH8 EXPDTA X-RAY DIFFRACTION AUTHOR W.SCOTT,B.LOWRANCE,A.C.ANDERSON,J.T.WEADGE REVDAT 3 11-OCT-23 6UJF 1 REMARK REVDAT 2 09-DEC-20 6UJF 1 JRNL REVDAT 1 14-OCT-20 6UJF 0 JRNL AUTH W.SCOTT,B.LOWRANCE,A.C.ANDERSON,J.T.WEADGE JRNL TITL IDENTIFICATION OF THE CLOSTRIDIAL CELLULOSE SYNTHASE AND JRNL TITL 2 CHARACTERIZATION OF THE COGNATE GLYCOSYL HYDROLASE, CCSZ. JRNL REF PLOS ONE V. 15 42686 2020 JRNL REFN ESSN 1932-6203 JRNL PMID 33264329 JRNL DOI 10.1371/JOURNAL.PONE.0242686 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.69 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 21745 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.237 REMARK 3 R VALUE (WORKING SET) : 0.235 REMARK 3 FREE R VALUE : 0.282 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1089 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 31.6920 - 3.9977 1.00 2676 141 0.1724 0.1950 REMARK 3 2 3.9977 - 3.1740 1.00 2604 137 0.2118 0.2616 REMARK 3 3 3.1740 - 2.7731 1.00 2571 136 0.2636 0.3512 REMARK 3 4 2.7731 - 2.5197 0.99 2576 136 0.2986 0.3880 REMARK 3 5 2.5197 - 2.3391 0.99 2546 133 0.2896 0.3668 REMARK 3 6 2.3391 - 2.2012 0.99 2544 135 0.3233 0.3535 REMARK 3 7 2.2012 - 2.0910 1.00 2570 135 0.3202 0.3954 REMARK 3 8 2.0910 - 2.0000 1.00 2569 136 0.3722 0.4005 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.320 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 37.240 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 48.53 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.29 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 6UJF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-OCT-19. REMARK 100 THE DEPOSITION ID IS D_1000244681. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JUN-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : ACCEL/BRUKER DCM REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25294 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 31.692 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.01846 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.9600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.28360 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MRBUMP REMARK 200 STARTING MODEL: 3UJE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MES, 200 MM CALCIUM ACETATE, REMARK 280 20% (V/V) POLY(ETHYLENE GLYCOL) 8000, 2.5 MM CELLOTRIOSE, PH 6.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 23.26500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 MET A 31 REMARK 465 ARG A 32 REMARK 465 ASP A 33 REMARK 465 ASN A 34 REMARK 465 SER A 35 REMARK 465 ASP A 36 REMARK 465 THR A 37 REMARK 465 VAL A 38 REMARK 465 SER A 91 REMARK 465 LYS A 341 REMARK 465 ARG A 342 REMARK 465 LEU A 343 REMARK 465 GLU A 344 REMARK 465 HIS A 345 REMARK 465 HIS A 346 REMARK 465 HIS A 347 REMARK 465 HIS A 348 REMARK 465 HIS A 349 REMARK 465 HIS A 350 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 LYS A 41 -65.48 -146.08 REMARK 500 ALA A 49 -97.01 -117.72 REMARK 500 GLU A 167 -116.50 64.02 REMARK 500 PHE A 201 35.54 77.55 REMARK 500 ASP A 215 125.54 179.73 REMARK 500 ASN A 217 66.33 -106.24 REMARK 500 TYR A 225 29.69 -146.37 REMARK 500 ASN A 274 67.38 39.77 REMARK 500 GLU A 315 127.54 121.78 REMARK 500 SER A 318 -143.82 -115.62 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 TRP A 314 GLU A 315 130.70 REMARK 500 REMARK 500 REMARK: NULL REMARK 999 REMARK 999 SEQUENCE REMARK 999 THERE IS NO UNIPROT SEQUENCE AVAILABLE AT THE TIME OF PROCESSING. REMARK 999 THE DEPOSITED SEQUENCE CORRESPONDS TO THE GENBANK ENTRY WP_ REMARK 999 077724661.1. DBREF 6UJF A 31 350 PDB 6UJF 6UJF 31 350 SEQRES 1 A 320 MET ARG ASP ASN SER ASP THR VAL LYS MET LYS ARG GLY SEQRES 2 A 320 ILE ASN ILE GLY ASN ALA LEU GLU SER PRO LYS ASP PHE SEQRES 3 A 320 PRO TRP ASP VAL LYS MET SER ASN LYS PHE PHE ASP ASP SEQRES 4 A 320 ILE LYS ASP ALA GLY PHE ASP THR VAL ARG ILE PRO VAL SEQRES 5 A 320 ARG PHE SER ASP TYR THR SER ASP SER ASP ASN PHE LYS SEQRES 6 A 320 ILE ASP GLU ASP PHE PHE LYS LYS ILE ASP LYS TYR VAL SEQRES 7 A 320 ASP TYR ALA LEU ASP LYS ASP LEU ILE VAL VAL LEU ASP SEQRES 8 A 320 LEU HIS HIS PHE GLU GLU ILE MET LYS GLU PRO ARG VAL SEQRES 9 A 320 HIS LYS GLU LYS PHE LEU LYS ILE TRP GLN GLN ILE ALA SEQRES 10 A 320 ASN ARG TYR GLN LYS TYR ASP LYS LYS LEU VAL PHE GLU SEQRES 11 A 320 LEU LEU ASN GLU PRO LYS GLU ASN LEU TYR SER GLN LEU SEQRES 12 A 320 LEU ASN GLU TYR ILE GLU GLU ALA ILE LYS ILE ILE ARG SEQRES 13 A 320 LYS THR ASN PRO LYS ARG THR ILE ILE VAL GLY PRO TYR SEQRES 14 A 320 ASN PHE TYR GLN ILE ASP TYR LEU ASN GLU LEU ASN ILE SEQRES 15 A 320 PRO LYS ASP SER ASN ILE VAL VAL SER PHE HIS TYR TYR SEQRES 16 A 320 GLU PRO ASN ASP PHE ALA PHE GLN GLY ASN ILE TYR HIS SEQRES 17 A 320 LYS GLY PHE GLU HIS LEU SER ASN ILE THR TRP GLU GLY SEQRES 18 A 320 THR ASN GLU GLN MET ASP TYR LEU LYS LYS ARG PHE ASP SEQRES 19 A 320 THR VAL GLU ASN TRP ALA ASN LYS ASN ASN VAL LYS ILE SEQRES 20 A 320 PHE LEU GLY GLU PHE GLY VAL THR LYS GLU ALA PRO GLU SEQRES 21 A 320 THR SER ARG ARG ALA TRP VAL LYS ALA VAL ARG GLU GLU SEQRES 22 A 320 ALA GLU LYS ARG ASN PHE SER TRP ALA TYR TRP GLU LEU SEQRES 23 A 320 ALA SER GLY PHE GLY ILE TYR ASN GLN ILE GLU GLY THR SEQRES 24 A 320 TRP ASP ARG ASP ILE LEU SER ALA LEU ILE GLU LYS ARG SEQRES 25 A 320 LEU GLU HIS HIS HIS HIS HIS HIS HET BGC A 401 12 HETNAM BGC BETA-D-GLUCOPYRANOSE HETSYN BGC BETA-D-GLUCOSE; D-GLUCOSE; GLUCOSE FORMUL 2 BGC C6 H12 O6 FORMUL 3 HOH *82(H2 O) HELIX 1 AA1 SER A 63 ALA A 73 1 11 HELIX 2 AA2 ARG A 83 THR A 88 5 6 HELIX 3 AA3 ASP A 97 ASP A 113 1 17 HELIX 4 AA4 PHE A 125 GLU A 131 1 7 HELIX 5 AA5 GLU A 131 TYR A 150 1 20 HELIX 6 AA6 TYR A 170 ASN A 189 1 20 HELIX 7 AA7 PRO A 198 GLN A 203 1 6 HELIX 8 AA8 ILE A 204 LEU A 210 5 7 HELIX 9 AA9 PRO A 227 GLN A 233 1 7 HELIX 10 AB1 THR A 252 ASN A 274 1 23 HELIX 11 AB2 PRO A 289 ARG A 307 1 19 HELIX 12 AB3 ASP A 331 ILE A 339 1 9 SHEET 1 AA1 9 ARG A 42 ASN A 45 0 SHEET 2 AA1 9 THR A 77 VAL A 82 1 O ARG A 79 N ILE A 44 SHEET 3 AA1 9 ILE A 117 LEU A 122 1 O ILE A 117 N VAL A 78 SHEET 4 AA1 9 LEU A 157 GLU A 160 1 O VAL A 158 N VAL A 118 SHEET 5 AA1 9 ILE A 194 VAL A 196 1 O ILE A 195 N PHE A 159 SHEET 6 AA1 9 ILE A 218 HIS A 223 1 O SER A 221 N VAL A 196 SHEET 7 AA1 9 LYS A 276 PHE A 282 1 O LYS A 276 N VAL A 220 SHEET 8 AA1 9 SER A 310 TYR A 313 1 O SER A 310 N LEU A 279 SHEET 9 AA1 9 ARG A 42 ASN A 45 1 N GLY A 43 O TYR A 313 SHEET 1 AA2 2 TYR A 323 ASN A 324 0 SHEET 2 AA2 2 THR A 329 TRP A 330 -1 O THR A 329 N ASN A 324 CISPEP 1 GLU A 226 PRO A 227 0 -4.06 CRYST1 57.020 46.530 61.090 90.00 94.50 90.00 P 1 21 1 2 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 0.017538 0.000000 0.001380 0.00000 SCALE2 0.000000 0.021492 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016420 0.00000