HEADER HYDROLASE 22-MAR-17 5XC4 TITLE CRYSTAL STRUCTURE OF GH45 ENDOGLUCANASE EG27II AT PH4.0, IN COMPLEX TITLE 2 WITH CELLOBIOSE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDO-BETA-1,4-GLUCANASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 17-195; COMPND 5 EC: 3.2.1.4; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AMPULLARIA CROSSEAN; SOURCE 3 ORGANISM_TAXID: 228791; SOURCE 4 GENE: EG27II; SOURCE 5 EXPRESSION_SYSTEM: KOMAGATAELLA PASTORIS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: KM71 KEYWDS CELLULASE, GLYCOSIDE HYDROLASE FAMILY 45, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR T.NOMURA,K.MIZUTANI,H.IWASE,N.TAKAHASHI,B.MIKAMI REVDAT 4 22-NOV-23 5XC4 1 HETSYN REVDAT 3 29-JUL-20 5XC4 1 COMPND REMARK HET HETNAM REVDAT 3 2 1 FORMUL LINK SITE ATOM REVDAT 2 24-APR-19 5XC4 1 JRNL REVDAT 1 28-MAR-18 5XC4 0 JRNL AUTH T.NOMURA,H.IWASE,N.SAKA,N.TAKAHASHI,B.MIKAMI,K.MIZUTANI JRNL TITL HIGH-RESOLUTION CRYSTAL STRUCTURES OF THE GLYCOSIDE JRNL TITL 2 HYDROLASE FAMILY 45 ENDOGLUCANASE EG27II FROM THE SNAIL JRNL TITL 3 AMPULLARIA CROSSEAN. JRNL REF ACTA CRYSTALLOGR D STRUCT V. 75 426 2019 JRNL REF 2 BIOL JRNL REFN ISSN 2059-7983 JRNL PMID 30988259 JRNL DOI 10.1107/S2059798319003000 REMARK 2 REMARK 2 RESOLUTION. 1.42 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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) : 1.42 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.20 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 29861 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.114 REMARK 3 R VALUE (WORKING SET) : 0.113 REMARK 3 FREE R VALUE : 0.148 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 1484 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 42.2218 - 3.1574 1.00 2761 131 0.1150 0.1165 REMARK 3 2 3.1574 - 2.5062 1.00 2623 151 0.1341 0.1578 REMARK 3 3 2.5062 - 2.1894 1.00 2595 145 0.1169 0.1633 REMARK 3 4 2.1894 - 1.9892 1.00 2581 131 0.0949 0.1499 REMARK 3 5 1.9892 - 1.8467 1.00 2546 135 0.0893 0.1322 REMARK 3 6 1.8467 - 1.7378 1.00 2557 131 0.0940 0.1350 REMARK 3 7 1.7378 - 1.6508 1.00 2575 116 0.0953 0.1352 REMARK 3 8 1.6508 - 1.5789 1.00 2511 144 0.0941 0.1823 REMARK 3 9 1.5789 - 1.5181 1.00 2569 126 0.1046 0.1804 REMARK 3 10 1.5181 - 1.4657 1.00 2537 138 0.1247 0.1816 REMARK 3 11 1.4657 - 1.4199 1.00 2522 136 0.1733 0.2456 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.410 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 : 0.012 1584 REMARK 3 ANGLE : 1.290 2183 REMARK 3 CHIRALITY : 0.103 221 REMARK 3 PLANARITY : 0.009 300 REMARK 3 DIHEDRAL : 21.193 615 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 5XC4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-MAR-17. REMARK 100 THE DEPOSITION ID IS D_1300003269. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-OCT-16 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29924 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.420 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 29.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.42 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.59800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 1WC2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG4000, 200MM KCL, 50MM MES, 10MM REMARK 280 CELLOBIOSE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K 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 17.38500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.66200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.65900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.66200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.38500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.65900 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: 510 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 SER A -4 REMARK 465 LEU A -3 REMARK 465 GLU A -2 REMARK 465 LYS A -1 REMARK 465 ASP A 179 REMARK 465 HIS A 180 REMARK 465 HIS A 181 REMARK 465 HIS A 182 REMARK 465 HIS A 183 REMARK 465 HIS A 184 REMARK 465 HIS A 185 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 0 CG CD NE CZ NH1 NH2 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 ASP A 27 -13.23 -147.14 REMARK 500 ASP A 41 38.59 -82.74 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5XBX RELATED DB: PDB REMARK 900 RELATED ID: 5XBU RELATED DB: PDB REMARK 900 RELATED ID: 5XCA RELATED DB: PDB REMARK 900 RELATED ID: 5XCB RELATED DB: PDB REMARK 900 RELATED ID: 5XC9 RELATED DB: PDB DBREF 5XC4 A 1 179 UNP A7KMF0 A7KMF0_9CAEN 17 195 SEQADV 5XC4 SER A -4 UNP A7KMF0 EXPRESSION TAG SEQADV 5XC4 LEU A -3 UNP A7KMF0 EXPRESSION TAG SEQADV 5XC4 GLU A -2 UNP A7KMF0 EXPRESSION TAG SEQADV 5XC4 LYS A -1 UNP A7KMF0 EXPRESSION TAG SEQADV 5XC4 ARG A 0 UNP A7KMF0 EXPRESSION TAG SEQADV 5XC4 HIS A 180 UNP A7KMF0 EXPRESSION TAG SEQADV 5XC4 HIS A 181 UNP A7KMF0 EXPRESSION TAG SEQADV 5XC4 HIS A 182 UNP A7KMF0 EXPRESSION TAG SEQADV 5XC4 HIS A 183 UNP A7KMF0 EXPRESSION TAG SEQADV 5XC4 HIS A 184 UNP A7KMF0 EXPRESSION TAG SEQADV 5XC4 HIS A 185 UNP A7KMF0 EXPRESSION TAG SEQRES 1 A 190 SER LEU GLU LYS ARG ALA GLN LEU CYS GLN PRO ASP ALA SEQRES 2 A 190 HIS GLY VAL ARG ARG PHE ASN GLY ARG PRO CYS ALA SER SEQRES 3 A 190 THR THR ARG TYR VAL ASP GLY HIS LYS GLY ALA CYS GLY SEQRES 4 A 190 CYS GLY GLN LYS GLY SER ASP THR PRO PHE PRO TRP ASN SEQRES 5 A 190 LEU GLN LYS HIS VAL THR ALA PRO SER GLU ARG TYR PHE SEQRES 6 A 190 ASP ASP GLY GLY SER ASN LEU TRP CYS GLY LYS ASN CYS SEQRES 7 A 190 GLY LYS CYS VAL ARG LEU THR PRO THR GLY GLY PHE VAL SEQRES 8 A 190 PRO GLY LYS GLY GLY ALA PRO PRO ASN HIS ASN PRO VAL SEQRES 9 A 190 VAL PHE MET VAL THR ASN ALA CYS PRO ILE ASN GLY ASN SEQRES 10 A 190 GLU GLU TRP CYS GLY ILE SER GLY LYS PRO GLY THR ASN SEQRES 11 A 190 HIS VAL ASN SER HIS GLY TYR GLU VAL HIS PHE ASP LEU SEQRES 12 A 190 GLN ASP GLN VAL GLY GLN VAL GLU ALA LEU HIS TRP ASP SEQRES 13 A 190 ASN PRO GLU VAL THR TRP GLU GLU VAL PRO CYS PRO GLY SEQRES 14 A 190 ASP LEU GLN ALA ASN TYR GLN GLN CYS GLU CYS HIS ASN SEQRES 15 A 190 SER ASP HIS HIS HIS HIS HIS HIS HET BGC B 1 12 HET BGC B 2 11 HET BGC C 1 12 HET BGC C 2 11 HETNAM BGC BETA-D-GLUCOPYRANOSE HETSYN BGC BETA-D-GLUCOSE; D-GLUCOSE; GLUCOSE FORMUL 2 BGC 4(C6 H12 O6) FORMUL 4 HOH *131(H2 O) HELIX 1 AA1 PRO A 45 LYS A 50 1 6 HELIX 2 AA2 SER A 56 ASP A 61 1 6 HELIX 3 AA3 ASN A 112 GLY A 117 1 6 HELIX 4 AA4 GLY A 143 HIS A 149 1 7 HELIX 5 AA5 PRO A 163 GLN A 171 1 9 SHEET 1 AA1 9 GLN A 5 PRO A 6 0 SHEET 2 AA1 9 ARG A 12 PHE A 14 -1 O ARG A 13 N GLN A 5 SHEET 3 AA1 9 ARG A 17 TYR A 25 -1 O ARG A 17 N PHE A 14 SHEET 4 AA1 9 VAL A 155 VAL A 160 -1 O VAL A 155 N ALA A 20 SHEET 5 AA1 9 CYS A 76 PRO A 81 -1 N ARG A 78 O GLU A 158 SHEET 6 AA1 9 VAL A 99 VAL A 103 -1 O VAL A 99 N LEU A 79 SHEET 7 AA1 9 VAL A 52 PRO A 55 1 N THR A 53 O MET A 102 SHEET 8 AA1 9 HIS A 135 GLN A 139 -1 O ASP A 137 N ALA A 54 SHEET 9 AA1 9 ARG A 17 TYR A 25 1 N THR A 23 O LEU A 138 SSBOND 1 CYS A 4 CYS A 19 1555 1555 2.01 SSBOND 2 CYS A 33 CYS A 73 1555 1555 1.99 SSBOND 3 CYS A 35 CYS A 173 1555 1555 2.03 SSBOND 4 CYS A 69 CYS A 175 1555 1555 2.01 SSBOND 5 CYS A 76 CYS A 162 1555 1555 2.03 SSBOND 6 CYS A 107 CYS A 116 1555 1555 2.01 LINK O4 BGC B 1 C1 BGC B 2 1555 1555 1.43 LINK O4 BGC C 1 C1 BGC C 2 1555 1555 1.44 CRYST1 34.770 47.318 93.324 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 0.028760 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021134 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010715 0.00000