HEADER ISOMERASE 21-OCT-13 3WKI TITLE CRYSTAL STRUCTURE OF CELLOBIOSE 2-EPIMERASE IN COMPLEX WITH TITLE 2 CELLOBIITOL COMPND MOL_ID: 1; COMPND 2 MOLECULE: CELLOBIOSE 2-EPIMERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CE; COMPND 5 EC: 5.1.3.11; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHODOTHERMUS MARINUS; SOURCE 3 ORGANISM_TAXID: 29549; SOURCE 4 STRAIN: JCM9785; SOURCE 5 GENE: CE; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET22B KEYWDS (ALPHA/ALPHA)6 BARREL FOLD, EPIMERASE, CARBOHYDRATE/SUGAR BINDING, KEYWDS 2 EPIMERIZATION, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR T.FUJIWARA,W.SABURI,I.TANAKA,M.YAO REVDAT 5 08-NOV-23 3WKI 1 HETSYN REVDAT 4 29-JUL-20 3WKI 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE ATOM REVDAT 3 26-FEB-14 3WKI 1 JRNL REVDAT 2 29-JAN-14 3WKI 1 JRNL REVDAT 1 25-DEC-13 3WKI 0 JRNL AUTH T.FUJIWARA,W.SABURI,H.MATSUI,H.MORI,M.YAO JRNL TITL STRUCTURAL INSIGHTS INTO THE EPIMERIZATION OF JRNL TITL 2 BETA-1,4-LINKED OLIGOSACCHARIDES CATALYZED BY CELLOBIOSE JRNL TITL 3 2-EPIMERASE, THE SOLE ENZYME EPIMERIZING NON-ANOMERIC JRNL TITL 4 HYDROXYL GROUPS OF UNMODIFIED SUGARS JRNL REF J.BIOL.CHEM. V. 289 3405 2014 JRNL REFN ISSN 0021-9258 JRNL PMID 24362032 JRNL DOI 10.1074/JBC.M113.531251 REMARK 2 REMARK 2 RESOLUTION. 2.19 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: DEV_1389) 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) : 2.19 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.07 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 18049 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 919 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 2.3067 - 2.1910 0.96 2293 126 0.2178 0.3037 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.620 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 3443 REMARK 3 ANGLE : 1.078 4684 REMARK 3 CHIRALITY : 0.074 484 REMARK 3 PLANARITY : 0.005 613 REMARK 3 DIHEDRAL : 14.199 1240 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 3WKI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-OCT-13. REMARK 100 THE DEPOSITION ID IS D_1000096449. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-FEB-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 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-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NUMERICAL LINK TYPE SI(111) REMARK 200 DOUBLE CRYSTAL MONOCHROMATOR, REMARK 200 LIQUID NITROGEN COOLING REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18054 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.190 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 (%) : 99.4 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.11200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.19 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.31 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.6 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 0.58600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX (AUTOMR: 1.7.1_743) REMARK 200 STARTING MODEL: PDB ENTRY 3WKF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM ACETATE BUFFER PH 4.5, REMARK 280 1.0M AMMONIUM HYDROGEN PHOSPHATE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 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 20.83750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.77050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.60800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.77050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.83750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.60800 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 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 MET A 1 REMARK 465 SER A 2 REMARK 465 ARG A 410 REMARK 465 SER A 411 REMARK 465 ARG A 412 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 OE2 GLU A 18 O HOH A 806 1.89 REMARK 500 OD2 ASP A 349 O HOH A 757 2.08 REMARK 500 O HOH A 690 O HOH A 691 2.13 REMARK 500 OE1 GLU A 226 O HOH A 801 2.14 REMARK 500 O HOH A 784 O HOH A 796 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 GLU A 365 -151.95 64.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3WKF RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH CELLOBIITOL DBREF 3WKI A 1 412 UNP F8WRK9 CEEP_RHOMR 1 412 SEQRES 1 A 412 MET SER THR GLU THR ILE PRO ASP VAL ARG ARG LEU ARG SEQRES 2 A 412 ALA LEU GLN ALA GLU VAL HIS GLU GLU LEU THR GLU ASN SEQRES 3 A 412 ILE LEU LYS PHE TRP ALA THR ARG THR HIS ASP PRO VAL SEQRES 4 A 412 HIS GLY GLY PHE VAL GLY ARG VAL GLY PRO ASP GLY ARG SEQRES 5 A 412 PRO HIS PRO GLU ALA PRO ARG GLY ALA ILE LEU ASN ALA SEQRES 6 A 412 ARG ILE LEU TRP THR PHE ALA ALA ALA TYR ARG GLN LEU SEQRES 7 A 412 GLY THR PRO LEU TYR ARG GLU MET ALA GLU ARG ALA TYR SEQRES 8 A 412 ARG TYR PHE VAL ARG HIS PHE VAL ASP ALA GLU HIS GLY SEQRES 9 A 412 GLY VAL TYR TRP MET VAL ALA ALA ASP GLY ARG PRO LEU SEQRES 10 A 412 ASP THR ARG LYS HIS VAL TYR ALA GLN SER PHE ALA ILE SEQRES 11 A 412 TYR ALA LEU SER GLU TRP HIS ARG ALA THR GLY GLY GLU SEQRES 12 A 412 ALA ALA LEU ALA LEU ALA ARG SER ILE TYR ASP LEU ILE SEQRES 13 A 412 GLU THR HIS CYS ALA ASP ARG VAL HIS GLY GLY TYR VAL SEQRES 14 A 412 GLU ALA CYS ASP ARG ALA TRP ARG PRO LEU GLU ASP ALA SEQRES 15 A 412 ARG LEU SER ALA LYS ASP ALA PRO GLU PRO ARG SER MET SEQRES 16 A 412 ASN THR HIS LEU HIS VAL LEU GLU ALA TYR ALA ASN LEU SEQRES 17 A 412 TYR ARG VAL TRP PRO GLU THR GLU LEU ALA ALA ARG LEU SEQRES 18 A 412 GLN ALA LEU ILE GLU LEU PHE LEU ARG ALA ILE TYR HIS SEQRES 19 A 412 PRO ALA THR GLY HIS LEU ILE LEU PHE PHE ASP GLU ARG SEQRES 20 A 412 TRP ARG PRO ARG SER ARG ALA VAL SER PHE GLY HIS ASP SEQRES 21 A 412 ILE GLU ALA SER TRP LEU LEU LEU GLU ALA VAL ASP VAL SEQRES 22 A 412 LEU GLY GLN ALA THR LEU ARG PRO ARG VAL GLN GLN ALA SEQRES 23 A 412 SER LEU HIS LEU ALA ARG ALA THR LEU ALA GLU GLY ARG SEQRES 24 A 412 ALA PRO ASP GLY SER LEU TYR TYR GLU ILE GLY GLU GLN SEQRES 25 A 412 GLY HIS LEU ASP THR ASP ARG HIS TRP TRP PRO GLN ALA SEQRES 26 A 412 GLU ALA LEU VAL GLY PHE LEU ASN ALA TYR GLN GLU SER SEQRES 27 A 412 GLY GLU VAL LEU PHE TYR GLU ALA ALA GLU ASP VAL TRP SEQRES 28 A 412 ARG TYR ILE ARG GLU ARG GLN ARG ASP THR ARG GLY GLY SEQRES 29 A 412 GLU TRP PHE ALA ARG VAL ARG ASP ASP GLY ALA PRO TYR SEQRES 30 A 412 PRO ASP ASP LYS VAL ASP PHE TRP LYS GLY PRO TYR HIS SEQRES 31 A 412 ASN GLY ARG ALA CYS LEU GLU ALA ILE GLN ARG LEU ARG SEQRES 32 A 412 HIS LEU LEU GLU HIS VAL ARG SER ARG HET GLO B 1 12 HET BGC B 2 11 HET CL A 501 1 HET PO4 A 504 5 HETNAM GLO D-GLUCOSE HETNAM BGC BETA-D-GLUCOPYRANOSE HETNAM CL CHLORIDE ION HETNAM PO4 PHOSPHATE ION HETSYN GLO D-GLUCOSE IN LINEAR FORM HETSYN BGC BETA-D-GLUCOSE; D-GLUCOSE; GLUCOSE FORMUL 2 GLO C6 H12 O6 FORMUL 2 BGC C6 H12 O6 FORMUL 3 CL CL 1- FORMUL 4 PO4 O4 P 3- FORMUL 5 HOH *231(H2 O) HELIX 1 1 ASP A 8 ASN A 26 1 19 HELIX 2 2 ASN A 26 THR A 35 1 10 HELIX 3 3 ALA A 61 GLY A 79 1 19 HELIX 4 4 THR A 80 PHE A 98 1 19 HELIX 5 5 VAL A 123 GLY A 141 1 19 HELIX 6 6 GLY A 142 ALA A 161 1 20 HELIX 7 7 MET A 195 TRP A 212 1 18 HELIX 8 8 GLU A 214 ILE A 232 1 19 HELIX 9 9 SER A 256 GLY A 275 1 20 HELIX 10 10 LEU A 279 GLY A 298 1 20 HELIX 11 11 TRP A 321 GLY A 339 1 19 HELIX 12 12 GLU A 340 ARG A 357 1 18 HELIX 13 13 PRO A 388 GLU A 407 1 20 SHEET 1 A 3 ARG A 59 GLY A 60 0 SHEET 2 A 3 MET A 109 VAL A 110 -1 O VAL A 110 N ARG A 59 SHEET 3 A 3 PRO A 116 ASP A 118 -1 O ASP A 118 N MET A 109 SHEET 1 B 2 LYS A 121 HIS A 122 0 SHEET 2 B 2 ALA A 171 CYS A 172 -1 O CYS A 172 N LYS A 121 SHEET 1 C 2 ARG A 193 SER A 194 0 SHEET 2 C 2 PHE A 243 PHE A 244 -1 O PHE A 244 N ARG A 193 SHEET 1 D 2 GLU A 308 ILE A 309 0 SHEET 2 D 2 LEU A 315 ASP A 316 -1 O ASP A 316 N GLU A 308 SHEET 1 E 2 ARG A 319 HIS A 320 0 SHEET 2 E 2 ARG A 369 VAL A 370 -1 O VAL A 370 N ARG A 319 LINK O4 GLO B 1 C1 BGC B 2 1555 1555 1.38 CRYST1 41.675 87.216 93.541 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 0.023995 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011466 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010690 0.00000