PDB Short entry for 4UTU HEADER ISOMERASE 23-JUL-14 4UTU TITLE STRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF THE N- TITLE 2 ACETYLMANNOSAMINE-6-PHOSPHATE 2-EPIMERASE FROM CLOSTRIDIUM TITLE 3 PERFRINGENS COMPND MOL_ID: 1; COMPND 2 MOLECULE: N-ACETYLMANNOSAMINE-6-PHOSPHATE 2-EPIMERASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: MANNAC-6-P EPIMERASE; COMPND 5 EC: 5.1.3.9; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: N-ACETYLMANNOSAMINE-6-PHOSPHATE BOUND TO MOLECULE A COMPND 8 AND B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CLOSTRIDIUM PERFRINGENS STR. 13; SOURCE 3 ORGANISM_TAXID: 195102; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VARIANT: ROSETTA; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET-YSBLIC KEYWDS ISOMERASE, SUGAR 2-EPIMERASE, SIALIC ACID, SUGAR PHOSPHATE, ENZYME KEYWDS 2 MECHANISM, CARBOHYDRATE, MUTAGENESIS, 1H NMR SPECTROSCOPY EXPDTA X-RAY DIFFRACTION AUTHOR M.C.PELISSIER,C.SEBBAN-KREUZER,F.GUERLESQUIN,J.A.BRANNIGAN, AUTHOR 2 G.J.DAVIES,Y.BOURNE,F.VINCENT REVDAT 4 10-JAN-24 4UTU 1 REMARK REVDAT 3 14-JAN-15 4UTU 1 JRNL REVDAT 2 29-OCT-14 4UTU 1 JRNL REVDAT 1 15-OCT-14 4UTU 0 JRNL AUTH M.C.PELISSIER,C.SEBBAN-KREUZER,F.GUERLESQUIN,J.A.BRANNIGAN, JRNL AUTH 2 G.J.DAVIES,Y.BOURNE,F.VINCENT JRNL TITL STRUCTURAL AND FUNCTIONAL CHARACTERIZATION OF THE JRNL TITL 2 CLOSTRIDIUM PERFRINGENS N-ACETYLMANNOSAMINE-6-PHOSPHATE JRNL TITL 3 2-EPIMERASE ESSENTIAL FOR THE SIALIC ACID SALVAGE PATHWAY JRNL REF J.BIOL.CHEM. V. 289 35215 2014 JRNL REFN ISSN 0021-9258 JRNL PMID 25320079 JRNL DOI 10.1074/JBC.M114.604272 REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 76612 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.141 REMARK 3 R VALUE (WORKING SET) : 0.140 REMARK 3 FREE R VALUE : 0.169 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1565 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.45 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.49 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5222 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.23 REMARK 3 BIN R VALUE (WORKING SET) : 0.1830 REMARK 3 BIN FREE R VALUE SET COUNT : 109 REMARK 3 BIN FREE R VALUE : 0.2230 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3502 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 40 REMARK 3 SOLVENT ATOMS : 498 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.42000 REMARK 3 B22 (A**2) : -0.07000 REMARK 3 B33 (A**2) : -0.31000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.49000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.054 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.058 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.038 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.745 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.975 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.962 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3737 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2527 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5081 ; 1.607 ; 1.988 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6275 ; 0.981 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 500 ; 5.415 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 154 ;34.755 ;25.260 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 712 ;12.770 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;21.166 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 604 ; 0.097 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4143 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 662 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 729 ; 0.226 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2778 ; 0.202 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1824 ; 0.176 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2002 ; 0.088 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 359 ; 0.151 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 14 ; 0.148 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 40 ; 0.225 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 55 ; 0.177 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 3082 ; 1.134 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 958 ; 0.273 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3835 ; 1.346 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1508 ; 2.524 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1226 ; 3.559 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A -8 A 4 REMARK 3 ORIGIN FOR THE GROUP (A): -5.4684 -4.6872 35.4694 REMARK 3 T TENSOR REMARK 3 T11: 0.0574 T22: 0.1221 REMARK 3 T33: 0.0894 T12: -0.0011 REMARK 3 T13: 0.0079 T23: -0.0064 REMARK 3 L TENSOR REMARK 3 L11: 2.8370 L22: 0.9549 REMARK 3 L33: 0.7439 L12: 0.3279 REMARK 3 L13: 1.3080 L23: -0.2081 REMARK 3 S TENSOR REMARK 3 S11: 0.0445 S12: 0.1706 S13: -0.0239 REMARK 3 S21: -0.1752 S22: -0.0963 S23: -0.1376 REMARK 3 S31: 0.2226 S32: 0.2420 S33: 0.0518 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 5 A 92 REMARK 3 ORIGIN FOR THE GROUP (A): 14.6256 -8.6382 37.6031 REMARK 3 T TENSOR REMARK 3 T11: 0.0196 T22: -0.0137 REMARK 3 T33: 0.0226 T12: -0.0095 REMARK 3 T13: -0.0298 T23: -0.0021 REMARK 3 L TENSOR REMARK 3 L11: 0.6411 L22: 0.9400 REMARK 3 L33: 1.3331 L12: -0.1028 REMARK 3 L13: -0.2556 L23: -0.2591 REMARK 3 S TENSOR REMARK 3 S11: 0.0262 S12: 0.0878 S13: -0.0241 REMARK 3 S21: -0.1562 S22: 0.0363 S23: 0.0840 REMARK 3 S31: 0.1723 S32: -0.0847 S33: -0.0624 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 93 A 207 REMARK 3 ORIGIN FOR THE GROUP (A): 14.1690 7.0193 33.8941 REMARK 3 T TENSOR REMARK 3 T11: 0.0284 T22: -0.0047 REMARK 3 T33: 0.0608 T12: 0.0140 REMARK 3 T13: -0.0051 T23: 0.0344 REMARK 3 L TENSOR REMARK 3 L11: 0.6179 L22: 1.0965 REMARK 3 L33: 1.4556 L12: -0.1623 REMARK 3 L13: -0.2804 L23: -0.0598 REMARK 3 S TENSOR REMARK 3 S11: 0.1037 S12: 0.1248 S13: 0.1384 REMARK 3 S21: -0.1618 S22: 0.0133 S23: 0.0979 REMARK 3 S31: -0.1477 S32: -0.0939 S33: -0.1169 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 208 A 220 REMARK 3 ORIGIN FOR THE GROUP (A): 28.3924 0.2305 53.5091 REMARK 3 T TENSOR REMARK 3 T11: 0.0243 T22: 0.0313 REMARK 3 T33: 0.0380 T12: -0.0418 REMARK 3 T13: 0.0090 T23: -0.0241 REMARK 3 L TENSOR REMARK 3 L11: 1.6665 L22: 1.3845 REMARK 3 L33: 4.2850 L12: 0.5593 REMARK 3 L13: 0.7565 L23: 2.3875 REMARK 3 S TENSOR REMARK 3 S11: 0.0861 S12: -0.0135 S13: 0.1261 REMARK 3 S21: -0.1468 S22: 0.0640 S23: -0.0397 REMARK 3 S31: -0.3096 S32: 0.3004 S33: -0.1501 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B -8 B 3 REMARK 3 ORIGIN FOR THE GROUP (A): 45.5474 -15.8748 68.3628 REMARK 3 T TENSOR REMARK 3 T11: 0.0745 T22: 0.1378 REMARK 3 T33: 0.1212 T12: -0.0144 REMARK 3 T13: -0.0012 T23: 0.0444 REMARK 3 L TENSOR REMARK 3 L11: 2.6649 L22: 1.3036 REMARK 3 L33: 1.4139 L12: -1.1833 REMARK 3 L13: 0.4941 L23: 0.7950 REMARK 3 S TENSOR REMARK 3 S11: 0.0389 S12: -0.2201 S13: -0.2923 REMARK 3 S21: 0.0303 S22: 0.0240 S23: 0.1279 REMARK 3 S31: 0.1866 S32: -0.3730 S33: -0.0629 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 4 B 95 REMARK 3 ORIGIN FOR THE GROUP (A): 25.5467 -16.8992 64.7665 REMARK 3 T TENSOR REMARK 3 T11: 0.0181 T22: 0.0418 REMARK 3 T33: 0.0284 T12: 0.0409 REMARK 3 T13: -0.0255 T23: 0.0010 REMARK 3 L TENSOR REMARK 3 L11: 0.7532 L22: 0.7067 REMARK 3 L33: 1.4659 L12: 0.0587 REMARK 3 L13: -0.1518 L23: -0.1284 REMARK 3 S TENSOR REMARK 3 S11: 0.0013 S12: -0.1233 S13: -0.0965 REMARK 3 S21: 0.0386 S22: 0.0428 S23: -0.0055 REMARK 3 S31: 0.2134 S32: 0.2046 S33: -0.0441 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 96 B 155 REMARK 3 ORIGIN FOR THE GROUP (A): 25.4666 -12.2005 80.9050 REMARK 3 T TENSOR REMARK 3 T11: 0.0647 T22: 0.1692 REMARK 3 T33: 0.0017 T12: 0.0202 REMARK 3 T13: -0.0228 T23: -0.0020 REMARK 3 L TENSOR REMARK 3 L11: 1.0576 L22: 1.1127 REMARK 3 L33: 1.5705 L12: -0.0054 REMARK 3 L13: -0.0920 L23: -0.1721 REMARK 3 S TENSOR REMARK 3 S11: 0.0545 S12: -0.3569 S13: -0.0412 REMARK 3 S21: 0.2524 S22: 0.0360 S23: -0.0115 REMARK 3 S31: 0.0530 S32: 0.2246 S33: -0.0905 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 156 B 220 REMARK 3 ORIGIN FOR THE GROUP (A): 22.7884 1.3014 67.8241 REMARK 3 T TENSOR REMARK 3 T11: 0.0433 T22: 0.0394 REMARK 3 T33: 0.0417 T12: -0.0196 REMARK 3 T13: 0.0171 T23: -0.0478 REMARK 3 L TENSOR REMARK 3 L11: 0.6123 L22: 0.3963 REMARK 3 L33: 1.6211 L12: -0.1024 REMARK 3 L13: 0.3709 L23: -0.3539 REMARK 3 S TENSOR REMARK 3 S11: 0.0359 S12: -0.1347 S13: 0.0961 REMARK 3 S21: 0.1176 S22: 0.0337 S23: 0.0116 REMARK 3 S31: -0.2027 S32: 0.1184 S33: -0.0696 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. LYS 221 IS DISORDERED REMARK 4 REMARK 4 4UTU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-JUL-14. REMARK 100 THE DEPOSITION ID IS D_1290061319. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 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 : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 78204 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 41.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 4.300 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.90 REMARK 200 R MERGE FOR SHELL (I) : 0.46000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 4UTT REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M PROPIONIC ACID, CACODYLATE, BIS REMARK 280 -TRIS PROPANE BUFFER PH 8.0 AND 25% (W/V) PEG 1500 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 41.07350 REMARK 290 SMTRY3 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -56.9 KCAL/MOL 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 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 O HOH A 2226 O HOH A 2227 1.77 REMARK 500 O HOH A 2100 O HOH A 2274 1.98 REMARK 500 O HOH A 2104 O HOH A 2105 2.01 REMARK 500 O HOH B 2048 O HOH B 2117 2.01 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG B 29 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG B 121 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG B 121 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES 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 SER A 23 126.79 172.95 REMARK 500 SER B 23 128.37 166.00 REMARK 500 ASN B 105 14.07 59.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: DSSP REMARK 700 THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 700 THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LRY A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LRY B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1221 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 1221 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4UTT RELATED DB: PDB REMARK 900 STRUCTURAL CHARACTERISATION OF NANE, MANNAC6P C2 EPIMERASE, FROM REMARK 900 CLOSTRIDIUM PERFINGENS REMARK 900 RELATED ID: 4UTW RELATED DB: PDB REMARK 900 STRUCTURAL CHARACTERISATION OF NANE, MANNAC6P C2 EPIMERASE, FROM REMARK 900 CLOSTRIDIUM PERFINGENS DBREF 4UTU A 1 220 UNP Q8XNZ3 NANE_CLOPE 1 220 DBREF 4UTU B 1 220 UNP Q8XNZ3 NANE_CLOPE 1 220 SEQADV 4UTU GLY A -8 UNP Q8XNZ3 EXPRESSION TAG SEQADV 4UTU SER A -7 UNP Q8XNZ3 EXPRESSION TAG SEQADV 4UTU SER A -6 UNP Q8XNZ3 EXPRESSION TAG SEQADV 4UTU HIS A -5 UNP Q8XNZ3 EXPRESSION TAG SEQADV 4UTU HIS A -4 UNP Q8XNZ3 EXPRESSION TAG SEQADV 4UTU HIS A -3 UNP Q8XNZ3 EXPRESSION TAG SEQADV 4UTU HIS A -2 UNP Q8XNZ3 EXPRESSION TAG SEQADV 4UTU HIS A -1 UNP Q8XNZ3 EXPRESSION TAG SEQADV 4UTU HIS A 0 UNP Q8XNZ3 EXPRESSION TAG SEQADV 4UTU ALA A 66 UNP Q8XNZ3 LYS 66 CONFLICT SEQADV 4UTU GLY B -8 UNP Q8XNZ3 EXPRESSION TAG SEQADV 4UTU SER B -7 UNP Q8XNZ3 EXPRESSION TAG SEQADV 4UTU SER B -6 UNP Q8XNZ3 EXPRESSION TAG SEQADV 4UTU HIS B -5 UNP Q8XNZ3 EXPRESSION TAG SEQADV 4UTU HIS B -4 UNP Q8XNZ3 EXPRESSION TAG SEQADV 4UTU HIS B -3 UNP Q8XNZ3 EXPRESSION TAG SEQADV 4UTU HIS B -2 UNP Q8XNZ3 EXPRESSION TAG SEQADV 4UTU HIS B -1 UNP Q8XNZ3 EXPRESSION TAG SEQADV 4UTU HIS B 0 UNP Q8XNZ3 EXPRESSION TAG SEQADV 4UTU ALA B 66 UNP Q8XNZ3 LYS 66 CONFLICT SEQRES 1 A 229 GLY SER SER HIS HIS HIS HIS HIS HIS MET LEU ASP VAL SEQRES 2 A 229 VAL LYS GLY ASN LEU ILE VAL SER CYS GLN ALA LEU SER SEQRES 3 A 229 ASP GLU PRO LEU HIS SER SER PHE ILE MET GLY ARG MET SEQRES 4 A 229 ALA ILE ALA ALA LYS GLN GLY GLY ALA ALA ALA ILE ARG SEQRES 5 A 229 ALA GLN GLY VAL ASN ASP ILE ASN GLU ILE LYS GLU VAL SEQRES 6 A 229 THR LYS LEU PRO ILE ILE GLY ILE ILE ALA ARG ASN TYR SEQRES 7 A 229 ASP ASP SER GLU ILE TYR ILE THR PRO THR MET LYS GLU SEQRES 8 A 229 VAL ASP GLU LEU LEU LYS THR ASP CYS GLU MET ILE ALA SEQRES 9 A 229 LEU ASP ALA THR LYS ARG LYS ARG PRO ASN GLY GLU ASN SEQRES 10 A 229 VAL LYS ASP LEU VAL ASP ALA ILE HIS ALA LYS GLY ARG SEQRES 11 A 229 LEU ALA MET ALA ASP ILE SER THR LEU GLU GLU GLY ILE SEQRES 12 A 229 GLU ALA GLU LYS LEU GLY PHE ASP CYS VAL SER THR THR SEQRES 13 A 229 LEU SER GLY TYR THR PRO TYR SER LYS GLN SER ASN SER SEQRES 14 A 229 VAL ASP PHE GLU LEU LEU GLU GLU LEU VAL LYS THR VAL SEQRES 15 A 229 LYS ILE PRO VAL ILE CYS GLU GLY ARG ILE ASN THR PRO SEQRES 16 A 229 GLU GLU LEU LYS LYS ALA LEU ASP LEU GLY ALA TYR SER SEQRES 17 A 229 ALA VAL VAL GLY GLY ALA ILE THR ARG PRO GLN GLN ILE SEQRES 18 A 229 THR LYS ARG PHE THR ASP ILE LEU SEQRES 1 B 229 GLY SER SER HIS HIS HIS HIS HIS HIS MET LEU ASP VAL SEQRES 2 B 229 VAL LYS GLY ASN LEU ILE VAL SER CYS GLN ALA LEU SER SEQRES 3 B 229 ASP GLU PRO LEU HIS SER SER PHE ILE MET GLY ARG MET SEQRES 4 B 229 ALA ILE ALA ALA LYS GLN GLY GLY ALA ALA ALA ILE ARG SEQRES 5 B 229 ALA GLN GLY VAL ASN ASP ILE ASN GLU ILE LYS GLU VAL SEQRES 6 B 229 THR LYS LEU PRO ILE ILE GLY ILE ILE ALA ARG ASN TYR SEQRES 7 B 229 ASP ASP SER GLU ILE TYR ILE THR PRO THR MET LYS GLU SEQRES 8 B 229 VAL ASP GLU LEU LEU LYS THR ASP CYS GLU MET ILE ALA SEQRES 9 B 229 LEU ASP ALA THR LYS ARG LYS ARG PRO ASN GLY GLU ASN SEQRES 10 B 229 VAL LYS ASP LEU VAL ASP ALA ILE HIS ALA LYS GLY ARG SEQRES 11 B 229 LEU ALA MET ALA ASP ILE SER THR LEU GLU GLU GLY ILE SEQRES 12 B 229 GLU ALA GLU LYS LEU GLY PHE ASP CYS VAL SER THR THR SEQRES 13 B 229 LEU SER GLY TYR THR PRO TYR SER LYS GLN SER ASN SER SEQRES 14 B 229 VAL ASP PHE GLU LEU LEU GLU GLU LEU VAL LYS THR VAL SEQRES 15 B 229 LYS ILE PRO VAL ILE CYS GLU GLY ARG ILE ASN THR PRO SEQRES 16 B 229 GLU GLU LEU LYS LYS ALA LEU ASP LEU GLY ALA TYR SER SEQRES 17 B 229 ALA VAL VAL GLY GLY ALA ILE THR ARG PRO GLN GLN ILE SEQRES 18 B 229 THR LYS ARG PHE THR ASP ILE LEU HET LRY A 301 19 HET CL A1221 1 HET LRY B 301 19 HET CL B1221 1 HETNAM LRY N-ACETYLMANNOSAMINE-6-PHOSPHATE HETNAM CL CHLORIDE ION FORMUL 3 LRY 2(C8 H16 N O9 P) FORMUL 4 CL 2(CL 1-) FORMUL 7 HOH *498(H2 O) HELIX 1 1 HIS A 0 LYS A 6 1 7 HELIX 2 2 SER A 23 GLY A 37 1 15 HELIX 3 3 GLY A 46 LYS A 58 1 13 HELIX 4 4 THR A 79 LYS A 88 1 10 HELIX 5 5 ARG A 103 GLU A 107 5 5 HELIX 6 6 ASN A 108 LYS A 119 1 12 HELIX 7 7 THR A 129 LEU A 139 1 11 HELIX 8 8 ASP A 162 VAL A 173 1 12 HELIX 9 9 THR A 185 LEU A 195 1 11 HELIX 10 10 GLY A 203 ARG A 208 1 6 HELIX 11 11 ARG A 208 ASP A 218 1 11 HELIX 12 12 HIS B 0 LYS B 6 1 7 HELIX 13 13 SER B 23 GLY B 37 1 15 HELIX 14 14 GLY B 46 LYS B 58 1 13 HELIX 15 15 THR B 79 LYS B 88 1 10 HELIX 16 16 ARG B 103 GLU B 107 5 5 HELIX 17 17 ASN B 108 LYS B 119 1 12 HELIX 18 18 THR B 129 LEU B 139 1 11 HELIX 19 19 ASP B 162 LYS B 171 1 10 HELIX 20 20 THR B 185 LEU B 195 1 11 HELIX 21 21 GLY B 203 ARG B 208 1 6 HELIX 22 22 ARG B 208 ILE B 219 1 12 SHEET 1 AA 9 LEU A 9 SER A 12 0 SHEET 2 AA 9 SER A 199 VAL A 202 1 O ALA A 200 N ILE A 10 SHEET 3 AA 9 VAL A 177 GLU A 180 1 O CYS A 179 N VAL A 201 SHEET 4 AA 9 CYS A 143 SER A 145 1 O VAL A 144 N ILE A 178 SHEET 5 AA 9 LEU A 122 ASP A 126 1 O ALA A 125 N SER A 145 SHEET 6 AA 9 MET A 93 ASP A 97 1 O ILE A 94 N MET A 124 SHEET 7 AA 9 ILE A 61 ILE A 64 1 O ILE A 61 N MET A 93 SHEET 8 AA 9 ALA A 41 GLN A 45 1 O ILE A 42 N ILE A 62 SHEET 9 AA 9 LEU A 9 SER A 12 1 O VAL A 11 N ARG A 43 SHEET 1 BA 9 LEU B 9 SER B 12 0 SHEET 2 BA 9 SER B 199 VAL B 202 1 O ALA B 200 N ILE B 10 SHEET 3 BA 9 VAL B 177 GLU B 180 1 O CYS B 179 N VAL B 201 SHEET 4 BA 9 CYS B 143 SER B 145 1 O VAL B 144 N ILE B 178 SHEET 5 BA 9 LEU B 122 ASP B 126 1 O ALA B 125 N SER B 145 SHEET 6 BA 9 MET B 93 ASP B 97 1 O ILE B 94 N MET B 124 SHEET 7 BA 9 ILE B 61 ILE B 64 1 O ILE B 61 N MET B 93 SHEET 8 BA 9 ALA B 41 GLN B 45 1 O ILE B 42 N ILE B 62 SHEET 9 BA 9 LEU B 9 SER B 12 1 O VAL B 11 N ARG B 43 SITE 1 AC1 21 GLN A 14 ARG A 43 TYR A 75 THR A 147 SITE 2 AC1 21 TYR A 151 GLU A 180 GLY A 181 ARG A 182 SITE 3 AC1 21 GLY A 203 GLY A 204 ARG A 208 HOH A2055 SITE 4 AC1 21 HOH A2058 HOH A2198 HOH A2202 HOH A2235 SITE 5 AC1 21 HOH A2236 HOH A2256 HOH A2261 HOH A2274 SITE 6 AC1 21 HOH A2275 SITE 1 AC2 22 GLN B 14 ARG B 43 ILE B 64 TYR B 75 SITE 2 AC2 22 THR B 147 TYR B 151 GLU B 180 GLY B 181 SITE 3 AC2 22 ARG B 182 GLY B 203 GLY B 204 ARG B 208 SITE 4 AC2 22 HOH B2030 HOH B2033 HOH B2161 HOH B2165 SITE 5 AC2 22 HOH B2185 HOH B2186 HOH B2202 HOH B2210 SITE 6 AC2 22 HOH B2222 HOH B2223 SITE 1 AC3 5 ARG A 208 PRO A 209 GLN A 210 HOH A2069 SITE 2 AC3 5 HOH A2070 SITE 1 AC4 5 ARG B 208 PRO B 209 GLN B 210 HOH B2045 SITE 2 AC4 5 HOH B2049 CRYST1 36.714 82.147 75.195 90.00 92.48 90.00 P 1 21 1 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 0.027238 0.000000 0.001180 0.00000 SCALE2 0.000000 0.012173 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013311 0.00000