HEADER HYDROLASE 22-DEC-14 3X2G TITLE X-RAY STRUCTURE OF PCCEL45A N92D APO FORM AT 100K 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 3X2G 1 JRNL SEQADV REVDAT 1 07-OCT-15 3X2G 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. 1.00 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) : 1.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.48 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 90553 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.098 REMARK 3 R VALUE (WORKING SET) : 0.097 REMARK 3 FREE R VALUE : 0.109 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.020 REMARK 3 FREE R VALUE TEST SET COUNT : 9075 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 18.4869 - 3.1030 0.92 2718 284 0.1501 0.1645 REMARK 3 2 3.1030 - 2.4648 1.00 2825 300 0.1199 0.1324 REMARK 3 3 2.4648 - 2.1537 1.00 2777 306 0.1134 0.1302 REMARK 3 4 2.1537 - 1.9571 1.00 2779 303 0.0977 0.0990 REMARK 3 5 1.9571 - 1.8169 1.00 2750 294 0.0993 0.1105 REMARK 3 6 1.8169 - 1.7099 1.00 2744 306 0.0948 0.1007 REMARK 3 7 1.7099 - 1.6243 1.00 2707 334 0.0917 0.1116 REMARK 3 8 1.6243 - 1.5536 1.00 2771 297 0.0880 0.1001 REMARK 3 9 1.5536 - 1.4939 1.00 2723 290 0.0823 0.0981 REMARK 3 10 1.4939 - 1.4423 1.00 2719 301 0.0847 0.0946 REMARK 3 11 1.4423 - 1.3972 1.00 2780 267 0.0805 0.0962 REMARK 3 12 1.3972 - 1.3573 1.00 2731 305 0.0781 0.0835 REMARK 3 13 1.3573 - 1.3216 1.00 2703 272 0.0775 0.1028 REMARK 3 14 1.3216 - 1.2894 1.00 2723 315 0.0784 0.0966 REMARK 3 15 1.2894 - 1.2601 1.00 2681 293 0.0764 0.0893 REMARK 3 16 1.2601 - 1.2332 1.00 2713 316 0.0750 0.0857 REMARK 3 17 1.2332 - 1.2086 1.00 2707 310 0.0730 0.0878 REMARK 3 18 1.2086 - 1.1858 1.00 2698 316 0.0712 0.0888 REMARK 3 19 1.1858 - 1.1646 1.00 2704 310 0.0669 0.0784 REMARK 3 20 1.1646 - 1.1449 1.00 2657 314 0.0653 0.0757 REMARK 3 21 1.1449 - 1.1264 1.00 2697 309 0.0701 0.0832 REMARK 3 22 1.1264 - 1.1091 1.00 2684 315 0.0693 0.0796 REMARK 3 23 1.1091 - 1.0928 1.00 2694 301 0.0736 0.0864 REMARK 3 24 1.0928 - 1.0774 1.00 2706 300 0.0795 0.0968 REMARK 3 25 1.0774 - 1.0628 1.00 2711 299 0.0798 0.0906 REMARK 3 26 1.0628 - 1.0490 1.00 2700 293 0.0841 0.0961 REMARK 3 27 1.0490 - 1.0359 1.00 2639 320 0.0853 0.1118 REMARK 3 28 1.0359 - 1.0234 1.00 2706 294 0.0944 0.1086 REMARK 3 29 1.0234 - 1.0115 1.00 2670 305 0.0964 0.1167 REMARK 3 30 1.0115 - 1.0000 0.99 2661 306 0.1036 0.1224 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) : 0.040 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 6.910 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 1437 REMARK 3 ANGLE : 1.331 1957 REMARK 3 CHIRALITY : 0.077 194 REMARK 3 PLANARITY : 0.008 270 REMARK 3 DIHEDRAL : 18.108 494 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 3X2G 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_1000097094. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-FEB-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 90937 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.000 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 8.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.02700 REMARK 200 FOR THE DATA SET : 43.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.20500 REMARK 200 FOR SHELL : 7.400 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 (%): 46.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 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 28.99800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.54650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.80600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.54650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.99800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.80600 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 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 1.81 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 10.49 -141.89 REMARK 500 ASN A 63 13.72 -141.89 REMARK 500 ALA A 171 -91.94 -128.51 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 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 40S A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 40S A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS A 204 DBREF 3X2G A 1 180 UNP B3Y002 B3Y002_PHACH 27 206 SEQADV 3X2G 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 HET 40S A 202 8 HET 40S A 203 16 HET TRS A 204 8 HETNAM 40S 3-METHYLPENTANE-1,5-DIOL HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN TRS TRIS BUFFER FORMUL 2 40S 3(C6 H14 O2) FORMUL 5 TRS C4 H12 N O3 1+ FORMUL 6 HOH *266(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 GLY A 120 PHE A 126 1 7 HELIX 4 4 SER A 141 TRP A 145 5 5 HELIX 5 5 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 2.04 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 2.03 SSBOND 5 CYS A 158 CYS A 172 1555 1555 2.04 CISPEP 1 GLY A 73 PRO A 74 0 4.62 CISPEP 2 TRP A 167 PRO A 168 0 4.72 SITE 1 AC1 5 ASN A 70 HOH A 311 HOH A 326 HOH A 394 SITE 2 AC1 5 HOH A 519 SITE 1 AC2 7 ALA A 29 ALA A 30 HOH A 338 HOH A 368 SITE 2 AC2 7 HOH A 374 HOH A 391 HOH A 476 SITE 1 AC3 10 PRO A 74 PHE A 75 GLY A 76 GLN A 77 SITE 2 AC3 10 ALA A 123 LYS A 124 PHE A 126 PRO A 127 SITE 3 AC3 10 HOH A 354 HOH A 514 SITE 1 AC4 6 THR A 16 MET A 17 ASP A 92 ASP A 114 SITE 2 AC4 6 HOH A 466 HOH A 521 CRYST1 57.996 45.612 63.093 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 0.017243 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021924 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015850 0.00000