HEADER ISOMERASE 10-SEP-23 8WBV TITLE THE CRYSTAL STRUCTURE OF LINEAR MANNOSE WITH MUTANT H247F OF THE TITLE 2 CELLOBIOSE 2-EPIMERASE FROM CALDICELLULOSIRUPTOR SACCHAROLYTICUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: CELLOBIOSE 2-EPIMERASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CALDICELLULOSIRUPTOR SACCHAROLYTICUS; SOURCE 3 ORGANISM_TAXID: 351627; SOURCE 4 STRAIN: ATCC 43494 / DSM 8903 / TP8T 6331; SOURCE 5 GENE: CSAC_0294; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS CELLOBIOSE 2-EPIMERASE, BIOSYNTHETIC PROTEIN, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR R.J.YANG,Y.H.FENG REVDAT 1 25-OCT-23 8WBV 0 JRNL AUTH R.J.YANG,Y.H.FENG JRNL TITL THE CRYSTAL STRUCTURE OF LINEAR MANNOSE WITH MUTANT H247F OF JRNL TITL 2 THE CELLOBIOSE 2-EPIMERASE FROM CALDICELLULOSIRUPTOR JRNL TITL 3 SACCHAROLYTICUS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829) 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.88 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.1 REMARK 3 NUMBER OF REFLECTIONS : 28274 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 1420 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 29.8770 - 4.1976 0.87 2704 134 0.1552 0.1912 REMARK 3 2 4.1976 - 3.3332 0.92 2715 142 0.1379 0.1803 REMARK 3 3 3.3332 - 2.9122 0.92 2711 123 0.1690 0.2441 REMARK 3 4 2.9122 - 2.6461 0.91 2634 136 0.1855 0.2782 REMARK 3 5 2.6461 - 2.4566 0.93 2695 141 0.1959 0.2227 REMARK 3 6 2.4566 - 2.3118 0.92 2635 148 0.2032 0.2771 REMARK 3 7 2.3118 - 2.1961 0.91 2603 158 0.2026 0.2614 REMARK 3 8 2.1961 - 2.1005 0.93 2684 130 0.2015 0.2809 REMARK 3 9 2.1005 - 2.0196 0.95 2709 146 0.2167 0.3029 REMARK 3 10 2.0196 - 1.9500 0.97 2764 162 0.2386 0.2849 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.720 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 3434 REMARK 3 ANGLE : 0.849 4632 REMARK 3 CHIRALITY : 0.049 484 REMARK 3 PLANARITY : 0.004 581 REMARK 3 DIHEDRAL : 2.669 2830 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 27.0411 1.0133 -9.3553 REMARK 3 T TENSOR REMARK 3 T11: 0.1517 T22: 0.1148 REMARK 3 T33: 0.1477 T12: -0.0007 REMARK 3 T13: -0.0013 T23: -0.0042 REMARK 3 L TENSOR REMARK 3 L11: 1.1453 L22: 0.9634 REMARK 3 L33: 1.1644 L12: -0.0272 REMARK 3 L13: -0.0750 L23: 0.2037 REMARK 3 S TENSOR REMARK 3 S11: 0.0347 S12: 0.0299 S13: -0.0792 REMARK 3 S21: -0.0277 S22: -0.0399 S23: 0.0176 REMARK 3 S31: 0.0664 S32: -0.0415 S33: 0.0045 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 8WBV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-SEP-23. REMARK 100 THE DEPOSITION ID IS D_1300040964. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-FEB-17 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL12-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28308 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.0 REMARK 200 DATA REDUNDANCY : 3.270 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.3500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.62 REMARK 200 R MERGE FOR SHELL (I) : 0.52100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.440 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 (%): 44.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.8M NACL,0.1TRIS-HCI PH 8.5, 32% REMARK 280 PEG3350, VAPOR DIFFUSION, HANGING 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 27.89500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.50500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.92500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.50500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.89500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.92500 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 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: 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 LYS A 17 -53.42 -120.59 REMARK 500 GLU A 94 169.15 72.87 REMARK 500 VAL A 230 -61.47 -107.19 REMARK 500 VAL A 230 -65.65 -103.95 REMARK 500 ASP A 233 -169.42 -75.33 REMARK 500 LYS A 241 91.71 -68.75 REMARK 500 ASN A 294 -65.67 -90.86 REMARK 500 GLU A 298 -106.24 55.81 REMARK 500 SER A 351 -164.12 -126.07 REMARK 500 GLU A 352 -111.37 -143.10 REMARK 500 REMARK 500 REMARK: NULL DBREF 8WBV A 1 389 UNP A4XGA6 A4XGA6_CALS8 1 389 SEQADV 8WBV GLY A -1 UNP A4XGA6 EXPRESSION TAG SEQADV 8WBV SER A 0 UNP A4XGA6 EXPRESSION TAG SEQADV 8WBV PHE A 247 UNP A4XGA6 HIS 247 ENGINEERED MUTATION SEQRES 1 A 391 GLY SER MET ASP ILE THR ARG PHE LYS GLU ASP LEU LYS SEQRES 2 A 391 ALA HIS LEU GLU GLU LYS ILE ILE PRO PHE TRP GLN SER SEQRES 3 A 391 LEU LYS ASP ASP GLU PHE GLY GLY TYR TYR GLY TYR MET SEQRES 4 A 391 ASP PHE ASN LEU ASN ILE ASP ARG LYS ALA GLN LYS GLY SEQRES 5 A 391 CYS ILE LEU ASN SER ARG ILE LEU TRP PHE PHE SER ALA SEQRES 6 A 391 CYS TYR ASN VAL LEU LYS SER GLU LYS CYS LYS GLU MET SEQRES 7 A 391 ALA PHE HIS ALA PHE GLU PHE LEU LYS ASN LYS PHE TRP SEQRES 8 A 391 ASP LYS GLU TYR GLU GLY LEU PHE TRP SER VAL SER HIS SEQRES 9 A 391 LYS GLY VAL PRO VAL ASP VAL THR LYS HIS VAL TYR VAL SEQRES 10 A 391 GLN ALA PHE GLY ILE TYR GLY LEU SER GLU TYR TYR GLU SEQRES 11 A 391 ALA SER GLY ASP GLU GLU ALA LEU HIS MET ALA LYS ARG SEQRES 12 A 391 LEU PHE GLU ILE LEU GLU THR LYS CYS LYS ARG GLU ASN SEQRES 13 A 391 GLY TYR THR GLU GLN PHE GLU ARG ASN TRP GLN GLU LYS SEQRES 14 A 391 GLU ASN ARG PHE LEU SER GLU ASN GLY VAL ILE ALA SER SEQRES 15 A 391 LYS THR MET ASN THR HIS LEU HIS VAL LEU GLU SER TYR SEQRES 16 A 391 THR ASN LEU TYR ARG LEU LEU LYS LEU ASP ASP VAL TYR SEQRES 17 A 391 GLU ALA LEU GLU TRP ILE VAL ARG LEU PHE VAL ASP LYS SEQRES 18 A 391 ILE TYR LYS LYS GLY THR GLY HIS PHE LYS VAL PHE CYS SEQRES 19 A 391 ASP ASP ASN TRP ASN GLU LEU ILE LYS ALA VAL SER TYR SEQRES 20 A 391 GLY PHE ASP ILE GLU ALA SER TRP LEU LEU ASP GLN ALA SEQRES 21 A 391 ALA LYS TYR LEU LYS ASP GLU LYS LEU LYS GLU GLU VAL SEQRES 22 A 391 GLU LYS LEU ALA LEU GLU VAL ALA GLN ILE THR LEU LYS SEQRES 23 A 391 GLU ALA PHE ASP GLY GLN SER LEU ILE ASN GLU MET ILE SEQRES 24 A 391 GLU ASP ARG ILE ASP ARG SER LYS ILE TRP TRP VAL GLU SEQRES 25 A 391 ALA GLU THR VAL VAL GLY PHE PHE ASN ALA TYR GLN LYS SEQRES 26 A 391 THR LYS GLU GLU LYS TYR LEU ASP ALA ALA ILE LYS THR SEQRES 27 A 391 TRP GLU PHE ILE LYS GLU HIS LEU VAL ASP ARG ARG LYS SEQRES 28 A 391 ASN SER GLU TRP LEU TRP LYS VAL ASN GLU ASP LEU GLU SEQRES 29 A 391 ALA VAL ASN MET PRO ILE VAL GLU GLN TRP LYS CYS PRO SEQRES 30 A 391 TYR HIS ASN GLY ARG MET CYS LEU GLU ILE ILE LYS ARG SEQRES 31 A 391 VAL HET DNO A 401 12 HET BMA A 402 12 HET EDO A 403 4 HETNAM DNO D-MANNOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM EDO 1,2-ETHANEDIOL HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 DNO C6 H12 O6 FORMUL 3 BMA C6 H12 O6 FORMUL 4 EDO C2 H6 O2 FORMUL 5 HOH *128(H2 O) HELIX 1 AA1 SER A 0 LYS A 17 1 18 HELIX 2 AA2 LYS A 17 SER A 24 1 8 HELIX 3 AA3 CYS A 51 LYS A 69 1 19 HELIX 4 AA4 SER A 70 PHE A 88 1 19 HELIX 5 AA5 VAL A 113 GLY A 131 1 19 HELIX 6 AA6 ASP A 132 CYS A 150 1 19 HELIX 7 AA7 MET A 183 LYS A 201 1 19 HELIX 8 AA8 LEU A 202 LYS A 219 1 18 HELIX 9 AA9 TYR A 245 LYS A 260 1 16 HELIX 10 AB1 ASP A 264 PHE A 287 1 24 HELIX 11 AB2 TRP A 307 LYS A 325 1 19 HELIX 12 AB3 GLU A 326 LEU A 344 1 19 HELIX 13 AB4 PRO A 375 VAL A 389 1 15 SHEET 1 AA1 3 LYS A 49 GLY A 50 0 SHEET 2 AA1 3 SER A 99 VAL A 100 -1 O VAL A 100 N LYS A 49 SHEET 3 AA1 3 PRO A 106 ASP A 108 -1 O VAL A 107 N SER A 99 SHEET 1 AA2 2 LYS A 111 HIS A 112 0 SHEET 2 AA2 2 GLN A 159 PHE A 160 -1 O PHE A 160 N LYS A 111 SHEET 1 AA3 2 LYS A 151 ARG A 152 0 SHEET 2 AA3 2 GLY A 155 TYR A 156 -1 O GLY A 155 N ARG A 152 SHEET 1 AA4 2 LYS A 181 THR A 182 0 SHEET 2 AA4 2 PHE A 231 CYS A 232 -1 O CYS A 232 N LYS A 181 SHEET 1 AA5 2 TYR A 221 LYS A 222 0 SHEET 2 AA5 2 HIS A 227 PHE A 228 -1 O HIS A 227 N LYS A 222 SHEET 1 AA6 3 ALA A 242 SER A 244 0 SHEET 2 AA6 3 GLU A 295 ILE A 297 -1 O MET A 296 N VAL A 243 SHEET 3 AA6 3 ARG A 300 ASP A 302 -1 O ASP A 302 N GLU A 295 SHEET 1 AA7 2 LYS A 305 ILE A 306 0 SHEET 2 AA7 2 LYS A 356 VAL A 357 -1 O VAL A 357 N LYS A 305 CRYST1 55.790 75.850 97.010 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 0.017924 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013184 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010308 0.00000