HEADER HYDROLASE 22-DEC-14 3X2I TITLE X-RAY STRUCTURE OF PCCEL45A N92D APO FORM AT 298K. 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 2 18-DEC-19 3X2I 1 JRNL SEQADV REVDAT 1 07-OCT-15 3X2I 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. 1.60 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.50 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.560 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 23719 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.126 REMARK 3 R VALUE (WORKING SET) : 0.124 REMARK 3 FREE R VALUE : 0.151 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2372 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 43.5166 - 4.1105 1.00 1382 154 0.1268 0.1509 REMARK 3 2 4.1105 - 3.2630 1.00 1296 144 0.1079 0.1178 REMARK 3 3 3.2630 - 2.8506 1.00 1298 144 0.1249 0.1302 REMARK 3 4 2.8506 - 2.5900 1.00 1258 140 0.1286 0.1384 REMARK 3 5 2.5900 - 2.4044 1.00 1272 141 0.1247 0.1597 REMARK 3 6 2.4044 - 2.2626 1.00 1271 141 0.1262 0.1376 REMARK 3 7 2.2626 - 2.1493 1.00 1242 139 0.1214 0.1661 REMARK 3 8 2.1493 - 2.0558 1.00 1278 141 0.1192 0.1873 REMARK 3 9 2.0558 - 1.9766 1.00 1236 138 0.1159 0.1483 REMARK 3 10 1.9766 - 1.9084 1.00 1259 140 0.1208 0.1592 REMARK 3 11 1.9084 - 1.8487 1.00 1246 138 0.1190 0.1775 REMARK 3 12 1.8487 - 1.7959 1.00 1242 138 0.1215 0.1485 REMARK 3 13 1.7959 - 1.7486 1.00 1256 140 0.1298 0.1801 REMARK 3 14 1.7486 - 1.7059 1.00 1235 137 0.1336 0.1875 REMARK 3 15 1.7059 - 1.6672 1.00 1259 140 0.1343 0.1693 REMARK 3 16 1.6672 - 1.6317 1.00 1232 137 0.1445 0.1792 REMARK 3 17 1.6317 - 1.5990 0.87 1085 120 0.1523 0.1868 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) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 12.440 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 : 0.016 1357 REMARK 3 ANGLE : 1.555 1851 REMARK 3 CHIRALITY : 0.085 190 REMARK 3 PLANARITY : 0.009 256 REMARK 3 DIHEDRAL : 11.461 453 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 3X2I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-JAN-15. REMARK 100 THE DEPOSITION ID IS D_1000097096. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-JUL-14 REMARK 200 TEMPERATURE (KELVIN) : 273 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23719 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 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 (%) : 99.2 REMARK 200 DATA REDUNDANCY : 13.30 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.11800 REMARK 200 FOR THE DATA SET : 17.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.3 REMARK 200 DATA REDUNDANCY IN SHELL : 11.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.25300 REMARK 200 FOR SHELL : 8.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 65% 3-METHYL-1,5-PENTANEDIOL, 50 MM REMARK 280 TRIS-HCL, PH 7.5, VAPOR DIFFUSION, SITTING 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 23.08600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.17800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.51350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.17800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.08600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.51350 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 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 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 GLN A 90 CG CD OE1 NE2 REMARK 470 GLN A 93 CB CG CD OE1 NE2 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 OH TYR A 67 OE2 GLU A 94 2.02 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 ASN A 63 11.01 -144.51 REMARK 500 ASN A 63 14.37 -144.51 REMARK 500 ALA A 171 -88.51 -126.76 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 40S A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3X2G RELATED DB: PDB REMARK 900 PCCEL45A N92D APO FORM AT 95K REMARK 900 RELATED ID: 3X2H RELATED DB: PDB REMARK 900 PCCEL45A N92D WITH CELLOPENTAOSE DBREF 3X2I A 1 180 UNP B3Y002 B3Y002_PHACH 27 206 SEQADV 3X2I ASP A 92 UNP B3Y002 ASN 118 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 ASP 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 ASP 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 40S A 201 8 HETNAM 40S 3-METHYLPENTANE-1,5-DIOL FORMUL 2 40S C6 H14 O2 FORMUL 3 HOH *131(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 ASP 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 ALA A 164 5 6 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 ASP 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 2.01 SSBOND 2 CYS A 26 CYS A 54 1555 1555 2.04 SSBOND 3 CYS A 57 CYS A 142 1555 1555 2.04 SSBOND 4 CYS A 87 CYS A 96 1555 1555 2.04 SSBOND 5 CYS A 158 CYS A 172 1555 1555 2.04 CISPEP 1 GLY A 73 PRO A 74 0 3.72 CISPEP 2 TRP A 167 PRO A 168 0 2.80 SITE 1 AC1 7 GLY A 4 VAL A 6 ASN A 63 THR A 72 SITE 2 AC1 7 PHE A 75 THR A 100 HOH A 333 CRYST1 46.172 59.027 64.356 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 0.021658 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016941 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015539 0.00000