HEADER HYDROLASE 24-MAR-17 5XCZ TITLE STRUCTURE OF THE CELLOBIOHYDROLASE CEL6A FROM PHANEROCHAETE TITLE 2 CHRYSOSPORIUM IN COMPLEX WITH CELLOBIOSE AT 2.1 ANGSTROM COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUCANASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 82-439; COMPND 5 EC: 3.2.1.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PHANEROCHAETE CHRYSOSPORIUM; SOURCE 3 ORGANISM_COMMON: WHITE-ROT FUNGUS; SOURCE 4 ORGANISM_TAXID: 5306; SOURCE 5 GENE: CEL6A; SOURCE 6 EXPRESSION_SYSTEM: KOMAGATAELLA PASTORIS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4922 KEYWDS GLYCOSIDEHYDROLASE FAMILY 6, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.TACHIOKA,A.NAKAMURA,T.ISHIDA,K.IGARASHI,M.SAMEJIMA REVDAT 2 29-JUL-20 5XCZ 1 COMPND REMARK HETNAM LINK REVDAT 2 2 1 SITE ATOM REVDAT 1 26-JUL-17 5XCZ 0 JRNL AUTH M.TACHIOKA,A.NAKAMURA,T.ISHIDA,K.IGARASHI,M.SAMEJIMA JRNL TITL CRYSTAL STRUCTURE OF A FAMILY 6 CELLOBIOHYDROLASE FROM THE JRNL TITL 2 BASIDIOMYCETE PHANEROCHAETE CHRYSOSPORIUM JRNL REF ACTA CRYSTALLOGR F STRUCT V. 73 398 2017 JRNL REF 2 BIOL COMMUN JRNL REFN ESSN 2053-230X JRNL PMID 28695848 JRNL DOI 10.1107/S2053230X17008093 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575) 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.90 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 18675 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.870 REMARK 3 FREE R VALUE TEST SET COUNT : 909 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 45.9096 - 3.8155 1.00 3131 164 0.1484 0.2164 REMARK 3 2 3.8155 - 3.0286 1.00 2966 162 0.1677 0.1939 REMARK 3 3 3.0286 - 2.6458 1.00 2965 154 0.1992 0.2827 REMARK 3 4 2.6458 - 2.4039 0.99 2913 151 0.1990 0.2804 REMARK 3 5 2.4039 - 2.2316 0.99 2913 129 0.2055 0.2583 REMARK 3 6 2.2316 - 2.1001 0.99 2878 149 0.2093 0.2647 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) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.070 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 : 0.007 2820 REMARK 3 ANGLE : 0.839 3871 REMARK 3 CHIRALITY : 0.053 434 REMARK 3 PLANARITY : 0.006 504 REMARK 3 DIHEDRAL : 3.605 1645 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 5XCZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-MAR-17. REMARK 100 THE DEPOSITION ID IS D_1300003296. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-DEC-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19086 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: NULL REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: POLYETHYLENE GLYCOL 3350, 2-METHYL-2,4 REMARK 280 -PENTANDIOL, CALCIUM ACETATE, ACETATE BUFFER,, VAPOR DIFFUSION, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 27.25100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.55800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.47550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 42.55800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.25100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.47550 REMARK 290 SMTRY3 4 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 TOTAL BURIED SURFACE AREA: 770 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13590 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 5.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 TYR A 164 70.62 -154.17 REMARK 500 ASP A 165 35.33 -152.22 REMARK 500 GLU A 214 74.73 53.65 REMARK 500 ASP A 216 -18.54 82.11 REMARK 500 TRP A 264 -82.63 -100.12 REMARK 500 ASN A 300 -164.26 -114.24 REMARK 500 PRO A 418 -168.30 -79.92 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5XCY RELATED DB: PDB DBREF 5XCZ A 82 439 UNP H3K419 H3K419_PHACH 82 439 SEQRES 1 A 358 SER ALA ASN ASN PRO TRP THR GLY PHE GLN ILE PHE LEU SEQRES 2 A 358 SER PRO TYR TYR ALA ASN GLU VAL ALA ALA ALA ALA LYS SEQRES 3 A 358 GLN ILE THR ASP PRO THR LEU SER SER LYS ALA ALA SER SEQRES 4 A 358 VAL ALA ASN ILE PRO THR PHE THR TRP LEU ASP SER VAL SEQRES 5 A 358 ALA LYS ILE PRO ASP LEU GLY THR TYR LEU ALA SER ALA SEQRES 6 A 358 SER ALA LEU GLY LYS SER THR GLY THR LYS GLN LEU VAL SEQRES 7 A 358 GLN ILE VAL ILE TYR ASP LEU PRO ASP ARG ASP CYS ALA SEQRES 8 A 358 ALA LYS ALA SER ASN GLY GLU PHE SER ILE ALA ASN ASN SEQRES 9 A 358 GLY GLN ALA ASN TYR GLU ASN TYR ILE ASP GLN ILE VAL SEQRES 10 A 358 ALA GLN ILE GLN GLN PHE PRO ASP VAL ARG VAL VAL ALA SEQRES 11 A 358 VAL ILE GLU PRO ASP SER LEU ALA ASN LEU VAL THR ASN SEQRES 12 A 358 LEU ASN VAL GLN LYS CYS ALA ASN ALA LYS THR THR TYR SEQRES 13 A 358 LEU ALA CYS VAL ASN TYR ALA LEU THR ASN LEU ALA LYS SEQRES 14 A 358 VAL GLY VAL TYR MET TYR MET ASP ALA GLY HIS ALA GLY SEQRES 15 A 358 TRP LEU GLY TRP PRO ALA ASN LEU SER PRO ALA ALA GLN SEQRES 16 A 358 LEU PHE THR GLN VAL TRP GLN ASN ALA GLY LYS SER PRO SEQRES 17 A 358 PHE ILE LYS GLY LEU ALA THR ASN VAL ALA ASN TYR ASN SEQRES 18 A 358 ALA LEU GLN ALA ALA SER PRO ASP PRO ILE THR GLN GLY SEQRES 19 A 358 ASN PRO ASN TYR ASP GLU ILE HIS TYR ILE ASN ALA LEU SEQRES 20 A 358 ALA PRO LEU LEU GLN GLN ALA GLY TRP ASP ALA THR PHE SEQRES 21 A 358 ILE VAL ASP GLN GLY ARG SER GLY VAL GLN ASN ILE ARG SEQRES 22 A 358 GLN GLN TRP GLY ASP TRP CYS ASN ILE LYS GLY ALA GLY SEQRES 23 A 358 PHE GLY THR ARG PRO THR THR ASN THR GLY SER GLN PHE SEQRES 24 A 358 ILE ASP SER ILE VAL TRP VAL LYS PRO GLY GLY GLU CYS SEQRES 25 A 358 ASP GLY THR SER ASN SER SER SER PRO ARG TYR ASP SER SEQRES 26 A 358 THR CYS SER LEU PRO ASP ALA ALA GLN PRO ALA PRO GLU SEQRES 27 A 358 ALA GLY THR TRP PHE GLN ALA TYR PHE GLN THR LEU VAL SEQRES 28 A 358 SER ALA ALA ASN PRO PRO LEU HET GLC B 1 12 HET BGC B 2 11 HET TRS A 503 16 HETNAM GLC ALPHA-D-GLUCOPYRANOSE HETNAM BGC BETA-D-GLUCOPYRANOSE HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN TRS TRIS BUFFER FORMUL 2 GLC C6 H12 O6 FORMUL 2 BGC C6 H12 O6 FORMUL 3 TRS C4 H12 N O3 1+ FORMUL 4 HOH *199(H2 O) HELIX 1 AA1 SER A 95 GLN A 108 1 14 HELIX 2 AA2 ASP A 111 VAL A 121 1 11 HELIX 3 AA3 ALA A 122 ILE A 124 5 3 HELIX 4 AA4 SER A 132 ALA A 134 5 3 HELIX 5 AA5 LYS A 135 GLY A 154 1 20 HELIX 6 AA6 SER A 181 ASN A 184 5 4 HELIX 7 AA7 ASN A 185 GLN A 202 1 18 HELIX 8 AA8 ASP A 216 ASN A 224 1 9 HELIX 9 AA9 VAL A 227 VAL A 251 1 25 HELIX 10 AB1 TRP A 267 ALA A 269 5 3 HELIX 11 AB2 ASN A 270 ALA A 285 1 16 HELIX 12 AB3 ASP A 310 GLN A 314 5 5 HELIX 13 AB4 ASP A 320 ALA A 335 1 16 HELIX 14 AB5 ASP A 405 LEU A 410 5 6 HELIX 15 AB6 PHE A 424 ALA A 434 1 11 SHEET 1 AA1 3 GLN A 91 ILE A 92 0 SHEET 2 AA1 3 GLN A 157 ILE A 163 1 O LEU A 158 N GLN A 91 SHEET 3 AA1 3 THR A 128 LEU A 130 1 N LEU A 130 O VAL A 162 SHEET 1 AA2 7 GLN A 91 ILE A 92 0 SHEET 2 AA2 7 GLN A 157 ILE A 163 1 O LEU A 158 N GLN A 91 SHEET 3 AA2 7 ARG A 208 ILE A 213 1 O VAL A 212 N ILE A 163 SHEET 4 AA2 7 TYR A 254 ASP A 258 1 O TYR A 254 N ALA A 211 SHEET 5 AA2 7 ILE A 291 THR A 296 1 O GLY A 293 N MET A 257 SHEET 6 AA2 7 THR A 340 ASP A 344 1 O ASP A 344 N THR A 296 SHEET 7 AA2 7 ILE A 381 VAL A 385 1 O VAL A 385 N VAL A 343 SSBOND 1 CYS A 171 CYS A 230 1555 1555 2.02 SSBOND 2 CYS A 361 CYS A 408 1555 1555 2.04 LINK O4 GLC B 1 C1 BGC B 2 1555 1555 1.43 CISPEP 1 GLN A 415 PRO A 416 0 -2.31 CISPEP 2 ASN A 436 PRO A 437 0 -1.11 CRYST1 54.502 66.951 85.116 90.00 90.00 90.00 P 21 21 21 4 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 0.018348 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014936 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011749 0.00000