HEADER HYDROLASE 22-DEC-14 3X2K TITLE X-RAY STRUCTURE OF PCCEL45A D114N WITH CELLOPENTAOSE AT 95K. COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDOGLUCANASE V-LIKE PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 27-206; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: 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 STRAIN: K-3; SOURCE 6 GENE: EGV, PCCEL45A; SOURCE 7 EXPRESSION_SYSTEM: PICHIA PASTORIS; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: KM71H; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PPICZA KEYWDS HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.NAKAMURA,T.ISHIDA,M.SAMEJIMA,K.IGARASHI REVDAT 3 29-JUL-20 3X2K 1 COMPND REMARK HET HETNAM REVDAT 3 2 1 HETSYN FORMUL LINK SITE REVDAT 3 3 1 ATOM REVDAT 2 18-DEC-19 3X2K 1 JRNL SEQADV LINK REVDAT 1 07-OCT-15 3X2K 0 JRNL AUTH A.NAKAMURA,T.ISHIDA,K.KUSAKA,T.YAMADA,S.FUSHINOBU,I.TANAKA, JRNL AUTH 2 S.KANEKO,K.OHTA,H.TANAKA,K.INAKA,Y.HIGUCHI,N.NIIMURA, JRNL AUTH 3 M.SAMEJIMA,K.IGARASHI JRNL TITL "NEWTON'S CRADLE" PROTON RELAY WITH AMIDE-IMIDIC ACID JRNL TITL 2 TAUTOMERIZATION IN INVERTING CELLULASE VISUALIZED BY NEUTRON JRNL TITL 3 CRYSTALLOGRAPHY. JRNL REF SCI ADV V. 1 00263 2015 JRNL REFN ESSN 2375-2548 JRNL PMID 26601228 JRNL DOI 10.1126/SCIADV.1500263 REMARK 2 REMARK 2 RESOLUTION. 1.18 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.9_1692) 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) : 1.18 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.45 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 47046 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.107 REMARK 3 R VALUE (WORKING SET) : 0.106 REMARK 3 FREE R VALUE : 0.131 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.260 REMARK 3 FREE R VALUE TEST SET COUNT : 2003 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 26.4551 - 2.8468 1.00 3432 153 0.1197 0.1228 REMARK 3 2 2.8468 - 2.2600 1.00 3284 142 0.1170 0.1446 REMARK 3 3 2.2600 - 1.9744 1.00 3267 149 0.0997 0.1304 REMARK 3 4 1.9744 - 1.7939 1.00 3241 140 0.1002 0.1202 REMARK 3 5 1.7939 - 1.6654 1.00 3217 144 0.0952 0.1380 REMARK 3 6 1.6654 - 1.5672 1.00 3207 147 0.0939 0.1234 REMARK 3 7 1.5672 - 1.4887 1.00 3201 138 0.0874 0.1288 REMARK 3 8 1.4887 - 1.4239 1.00 3196 140 0.0904 0.1201 REMARK 3 9 1.4239 - 1.3691 1.00 3202 157 0.0929 0.1196 REMARK 3 10 1.3691 - 1.3219 1.00 3195 134 0.0955 0.1191 REMARK 3 11 1.3219 - 1.2805 1.00 3179 141 0.1052 0.1376 REMARK 3 12 1.2805 - 1.2439 1.00 3190 137 0.1051 0.1458 REMARK 3 13 1.2439 - 1.2112 1.00 3173 144 0.1120 0.1603 REMARK 3 14 1.2112 - 1.1816 0.96 3059 137 0.1296 0.1656 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) : 0.070 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 11.210 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 1594 REMARK 3 ANGLE : 1.365 2186 REMARK 3 CHIRALITY : 0.082 248 REMARK 3 PLANARITY : 0.009 276 REMARK 3 DIHEDRAL : 17.607 562 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 3X2K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-JAN-15. REMARK 100 THE DEPOSITION ID IS D_1000097098. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-MAY-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NE3A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8 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 : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47795 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.180 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 14.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.12100 REMARK 200 FOR THE DATA SET : 41.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.18 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 71.6 REMARK 200 DATA REDUNDANCY IN SHELL : 11.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.45700 REMARK 200 FOR SHELL : 4.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 60% 3-METHYL-1,5-PENTANEDIOL, 50 MM REMARK 280 TRIS-HCL, 5MM CELLOPENTAOSE, PH 8.5, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 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 19.30800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.39600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.16150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.39600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.30800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.16150 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 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 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 ASN A 92 42.26 -141.86 REMARK 500 ALA A 171 -98.10 -142.40 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3X2G RELATED DB: PDB REMARK 900 RELATED ID: 3X2H RELATED DB: PDB REMARK 900 RELATED ID: 3X2I RELATED DB: PDB REMARK 900 RELATED ID: 3X2J RELATED DB: PDB REMARK 900 RELATED ID: 3X2L RELATED DB: PDB REMARK 900 RELATED ID: 3X2M RELATED DB: PDB REMARK 900 RELATED ID: 3X2N RELATED DB: PDB REMARK 900 RELATED ID: 3X2O RELATED DB: PDB REMARK 900 RELATED ID: 3X2P RELATED DB: PDB DBREF 3X2K A 1 180 UNP B3Y002 B3Y002_PHACH 27 206 SEQADV 3X2K ASN A 114 UNP B3Y002 ASP 140 ENGINEERED MUTATION SEQRES 1 A 180 ALA THR GLY GLY TYR VAL GLN GLN ALA THR GLY GLN ALA SEQRES 2 A 180 SER PHE THR MET TYR SER GLY CYS GLY SER PRO ALA CYS SEQRES 3 A 180 GLY LYS ALA ALA SER GLY PHE THR ALA ALA ILE ASN GLN SEQRES 4 A 180 LEU ALA PHE GLY SER ALA PRO GLY LEU GLY ALA GLY ASP SEQRES 5 A 180 ALA CYS GLY ARG CYS PHE ALA LEU THR GLY ASN HIS ASP SEQRES 6 A 180 PRO TYR SER PRO ASN TYR THR GLY PRO PHE GLY GLN THR SEQRES 7 A 180 ILE VAL VAL LYS VAL THR ASP LEU CYS PRO VAL GLN GLY SEQRES 8 A 180 ASN GLN GLU PHE CYS GLY GLN THR THR SER ASN PRO THR SEQRES 9 A 180 ASN GLN HIS GLY MET PRO PHE HIS PHE ASN ILE CYS GLU SEQRES 10 A 180 ASP THR GLY GLY SER ALA LYS PHE PHE PRO SER GLY HIS SEQRES 11 A 180 GLY ALA LEU THR GLY THR PHE THR GLU VAL SER CYS SER SEQRES 12 A 180 GLN TRP SER GLY SER ASP GLY GLY GLN LEU TRP ASN GLY SEQRES 13 A 180 ALA CYS LEU SER GLY GLU THR ALA PRO ASN TRP PRO SER SEQRES 14 A 180 THR ALA CYS GLY ASN LYS GLY THR ALA PRO SER HET GLC B 1 13 HET BGC B 2 13 HET BGC B 3 16 HET BGC B 4 12 HET BGC B 5 12 HET BGC C 1 13 HET BGC C 2 12 HET BGC C 3 12 HET BGC C 4 14 HET BGC C 5 12 HET 40S A 211 8 HET 40S A 212 8 HET 40S A 213 8 HET 40S A 214 8 HET 40S A 215 8 HET TRS A 216 8 HET TRS A 217 8 HETNAM GLC ALPHA-D-GLUCOPYRANOSE HETNAM BGC BETA-D-GLUCOPYRANOSE HETNAM 40S 3-METHYLPENTANE-1,5-DIOL HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN TRS TRIS BUFFER FORMUL 2 GLC C6 H12 O6 FORMUL 2 BGC 9(C6 H12 O6) FORMUL 4 40S 5(C6 H14 O2) FORMUL 9 TRS 2(C4 H12 N O3 1+) FORMUL 11 HOH *232(H2 O) HELIX 1 1 ALA A 1 TYR A 5 5 5 HELIX 2 2 GLN A 39 GLY A 43 1 5 HELIX 3 3 ASN A 92 GLY A 97 1 6 HELIX 4 4 GLY A 120 PHE A 126 1 7 HELIX 5 5 SER A 141 TRP A 145 5 5 HELIX 6 6 LEU A 159 THR A 163 5 5 SHEET 1 A 7 THR A 10 TYR A 18 0 SHEET 2 A 7 PHE A 111 CYS A 116 1 O ILE A 115 N THR A 16 SHEET 3 A 7 THR A 34 ASN A 38 -1 N ALA A 36 O ASN A 114 SHEET 4 A 7 ILE A 79 CYS A 87 1 O CYS A 87 N ILE A 37 SHEET 5 A 7 CYS A 57 HIS A 64 -1 N LEU A 60 O ILE A 79 SHEET 6 A 7 LEU A 133 VAL A 140 -1 O THR A 138 N ALA A 59 SHEET 7 A 7 THR A 10 TYR A 18 -1 N PHE A 15 O LEU A 133 SSBOND 1 CYS A 21 CYS A 116 1555 1555 2.07 SSBOND 2 CYS A 26 CYS A 54 1555 1555 2.04 SSBOND 3 CYS A 57 CYS A 142 1555 1555 2.05 SSBOND 4 CYS A 87 CYS A 96 1555 1555 2.06 SSBOND 5 CYS A 158 CYS A 172 1555 1555 2.06 LINK O4 GLC B 1 C1 BGC B 2 1555 1555 1.42 LINK O4 BGC B 2 C1 BGC B 3 1555 1555 1.42 LINK O4 BGC B 3 C1 BGC B 4 1555 1555 1.42 LINK O4 BGC B 4 C1 BGC B 5 1555 1555 1.42 LINK O4 BGC C 1 C1 BGC C 2 1555 1555 1.41 LINK O4 BGC C 2 C1 BGC C 3 1555 1555 1.40 LINK O4 BGC C 3 C1 BGC C 4 1555 1555 1.37 LINK O4 BGC C 4 C1 BGC C 5 1555 1555 1.42 CISPEP 1 GLY A 73 PRO A 74 0 3.45 CISPEP 2 GLY A 73 PRO A 74 0 1.49 CISPEP 3 TRP A 167 PRO A 168 0 9.47 CRYST1 38.616 58.323 62.792 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 0.025896 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017146 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015926 0.00000