HEADER HYDROLASE 15-DEC-22 8BZQ TITLE BETA-1,4-D-ENDOGLUCANASE CEL45A FROM GLOEOPHYLLUM TRABEUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDOGLUCANASE V-LIKE PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GLOEOPHYLLUM TRABEUM ATCC 11539; SOURCE 3 ORGANISM_TAXID: 670483; SOURCE 4 ATCC: 11539; SOURCE 5 GENE: GLOTRDRAFT_59933; SOURCE 6 EXPRESSION_SYSTEM: ASPERGILLUS NIDULANS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 162425; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: A773 KEYWDS ENDOGLUCANASE, GTCEL45A, GH45 FAMILY, CELLULASE, BROWN ROT, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR L.OKMANE,L.FITKIN,J.STAHLBERG REVDAT 3 13-MAR-24 8BZQ 1 JRNL REVDAT 2 14-FEB-24 8BZQ 1 JRNL REVDAT 1 22-NOV-23 8BZQ 0 JRNL AUTH L.OKMANE,L.FITKIN,M.SANDGREN,J.STAHLBERG JRNL TITL THE FIRST CRYSTAL STRUCTURE OF A FAMILY 45 GLYCOSIDE JRNL TITL 2 HYDROLASE FROM A BROWN-ROT FUNGUS, GLOEOPHYLLUM TRABEUM JRNL TITL 3 GTCEL45A. JRNL REF FEBS OPEN BIO V. 14 505 2024 JRNL REFN ESSN 2211-5463 JRNL PMID 38311343 JRNL DOI 10.1002/2211-5463.13774 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.440 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 31109 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.183 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.130 REMARK 3 FREE R VALUE TEST SET COUNT : 974 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 2.4900 - 1.9700 1.00 4328 135 0.1716 0.2044 REMARK 3 2 1.9700 - 1.7200 1.00 4306 142 0.1695 0.1943 REMARK 3 3 1.7200 - 1.5700 1.00 4291 134 0.1669 0.1774 REMARK 3 4 1.5700 - 1.4500 1.00 4305 144 0.1617 0.1753 REMARK 3 5 1.4500 - 1.3700 1.00 4285 140 0.1682 0.1999 REMARK 3 6 1.3700 - 1.3000 0.99 4248 144 0.1689 0.1701 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) : 0.063 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.165 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.63 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.27 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 : 0.006 1304 REMARK 3 ANGLE : 0.926 1787 REMARK 3 CHIRALITY : 0.080 184 REMARK 3 PLANARITY : 0.007 245 REMARK 3 DIHEDRAL : 6.372 193 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 8BZQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-DEC-22. REMARK 100 THE DEPOSITION ID IS D_1292127488. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JUN-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID30B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976254 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31123 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 45.760 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 12.84 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 9.510 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.19.2_4158 REMARK 200 STARTING MODEL: 5KJO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 29.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES 7.5, 20% PEG 3350, 3MM REMARK 280 NICL2, PROTEIN 14 MG/ML, PH 7.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K 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 24.20500 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 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 LEU A 1 REMARK 465 GLU A 2 REMARK 465 GLU A 3 REMARK 465 ARG A 4 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 SER A 183 O OG REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 334 O HOH A 403 2.16 REMARK 500 REMARK 500 REMARK: NULL 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 SER A 72 82.90 -153.26 REMARK 500 ASN A 95 70.02 -155.12 REMARK 500 SER A 172 172.85 175.98 REMARK 500 ALA A 174 -93.82 -114.25 REMARK 500 REMARK 500 REMARK: NULL DBREF 8BZQ A 1 183 UNP S7QB86 S7QB86_GLOTA 22 204 SEQRES 1 A 183 LEU GLU GLU ARG ALA THR GLY GLY TYR VAL GLN ASN PRO SEQRES 2 A 183 SER GLY SER ALA SER PHE THR MET TYR SER GLY CYS GLY SEQRES 3 A 183 SER PRO ALA CYS GLY GLU THR ALA SER GLY TYR THR ALA SEQRES 4 A 183 ALA MET ASN GLN LEU SER PHE GLY ALA GLY PRO GLY ALA SEQRES 5 A 183 GLY ALA GLY ASP ALA CYS GLY ARG CYS PHE ALA LEU THR SEQRES 6 A 183 GLY THR ALA ASP PRO TYR SER PRO SER TYR THR GLY PRO SEQRES 7 A 183 PHE HIS THR ILE VAL VAL LYS VAL THR ASP LEU CYS PRO SEQRES 8 A 183 VAL ALA GLY ASN GLN GLU TRP CYS GLY GLN THR THR SER SEQRES 9 A 183 ASN PRO ASN ASN GLN HIS GLY GLU PRO VAL HIS PHE ASP SEQRES 10 A 183 ILE CYS GLU ASP THR GLY GLY ALA GLY ALA PHE PHE PRO SEQRES 11 A 183 SER GLY HIS GLY ALA LEU THR GLY THR TYR ARG GLU VAL SEQRES 12 A 183 SER CYS SER GLN TRP SER GLY SER ASP GLY SER PRO LEU SEQRES 13 A 183 TRP THR GLY ALA CYS LEU SER GLY GLU SER ALA ALA ASN SEQRES 14 A 183 TRP PRO SER THR ALA CYS GLY ASN LYS GLY THR ALA PRO SEQRES 15 A 183 SER FORMUL 2 HOH *217(H2 O) HELIX 1 AA1 ALA A 5 TYR A 9 5 5 HELIX 2 AA2 GLN A 43 GLY A 47 1 5 HELIX 3 AA3 ASN A 95 GLY A 100 1 6 HELIX 4 AA4 GLY A 123 PHE A 129 1 7 HELIX 5 AA5 SER A 144 TRP A 148 5 5 HELIX 6 AA6 LEU A 162 ALA A 167 5 6 SHEET 1 AA1 7 SER A 14 TYR A 22 0 SHEET 2 AA1 7 HIS A 115 CYS A 119 1 O ILE A 118 N THR A 20 SHEET 3 AA1 7 THR A 38 ASN A 42 -1 N ALA A 40 O ASP A 117 SHEET 4 AA1 7 THR A 81 CYS A 90 1 O CYS A 90 N MET A 41 SHEET 5 AA1 7 CYS A 61 ALA A 68 -1 N LEU A 64 O ILE A 82 SHEET 6 AA1 7 LEU A 136 VAL A 143 -1 O THR A 137 N THR A 67 SHEET 7 AA1 7 SER A 14 TYR A 22 -1 N PHE A 19 O LEU A 136 SSBOND 1 CYS A 25 CYS A 119 1555 1555 2.06 SSBOND 2 CYS A 30 CYS A 58 1555 1555 2.04 SSBOND 3 CYS A 61 CYS A 145 1555 1555 2.07 SSBOND 4 CYS A 90 CYS A 99 1555 1555 2.05 SSBOND 5 CYS A 161 CYS A 175 1555 1555 2.04 CISPEP 1 GLY A 77 PRO A 78 0 4.04 CISPEP 2 TRP A 170 PRO A 171 0 2.27 CRYST1 28.970 48.410 45.790 90.00 92.21 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 0.034518 0.000000 0.001330 0.00000 SCALE2 0.000000 0.020657 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021855 0.00000