HEADER LYASE 18-JUL-12 3VVC TITLE CRYSTAL STRUCTURE OF CAPSULAR POLYSACCHARIDE SYNTHESIZING ENZYME CAPE TITLE 2 , K126E, IN APO FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAPSULAR POLYSACCHARIDE SYNTHESIS ENZYME CAP8E; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: 4.2.1.115; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 158878; SOURCE 4 STRAIN: MU50; SOURCE 5 GENE: CAPE; 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: PET28 KEYWDS ROSSMANN FOLD, SHORT-CHAIN DEHYDROGENASE/REDUCTASE, CAPSULAR KEYWDS 2 POLYSACCHARIDE SYNTHESIS, OXIDASE, EPIMERASE, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR T.MIYAFUSA,J.M.CAAVEIRO,Y.TANAKA,K.TSUMOTO REVDAT 4 20-MAR-24 3VVC 1 REMARK SEQADV REVDAT 3 22-NOV-17 3VVC 1 REMARK REVDAT 2 29-JAN-14 3VVC 1 JRNL REVDAT 1 12-JUN-13 3VVC 0 JRNL AUTH T.MIYAFUSA,J.M.CAAVEIRO,Y.TANAKA,M.E.TANNER,K.TSUMOTO JRNL TITL CRYSTAL STRUCTURE OF THE CAPSULAR POLYSACCHARIDE JRNL TITL 2 SYNTHESIZING PROTEIN CAPE OF STAPHYLOCOCCUS AUREUS. JRNL REF BIOSCI.REP. V. 33 463 2013 JRNL REFN ISSN 0144-8463 JRNL PMID 23611437 JRNL DOI 10.1042/BSR20130017 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.74 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 19080 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) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1022 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1317 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2960 REMARK 3 BIN FREE R VALUE SET COUNT : 72 REMARK 3 BIN FREE R VALUE : 0.3280 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2504 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 73 REMARK 3 SOLVENT ATOMS : 82 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.58 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.25000 REMARK 3 B22 (A**2) : -0.25000 REMARK 3 B33 (A**2) : 0.38000 REMARK 3 B12 (A**2) : -0.13000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.244 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.223 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.175 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.742 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.914 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2633 ; 0.017 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3566 ; 2.009 ; 1.998 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 322 ; 7.255 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 120 ;39.869 ;24.917 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 474 ;19.190 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;17.923 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 407 ; 0.126 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1936 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 163 REMARK 3 RESIDUE RANGE : A 201 A 225 REMARK 3 ORIGIN FOR THE GROUP (A): 2.2983 -21.5105 -12.9764 REMARK 3 T TENSOR REMARK 3 T11: 0.1936 T22: 0.1107 REMARK 3 T33: 0.0190 T12: 0.0268 REMARK 3 T13: -0.0074 T23: -0.0370 REMARK 3 L TENSOR REMARK 3 L11: 2.3516 L22: 1.8796 REMARK 3 L33: 1.9688 L12: -0.2543 REMARK 3 L13: -0.3203 L23: -0.0149 REMARK 3 S TENSOR REMARK 3 S11: 0.0750 S12: 0.2373 S13: -0.1727 REMARK 3 S21: -0.3089 S22: -0.0405 S23: -0.0264 REMARK 3 S31: 0.1665 S32: 0.0823 S33: -0.0345 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 166 A 199 REMARK 3 RESIDUE RANGE : A 227 A 282 REMARK 3 ORIGIN FOR THE GROUP (A): -2.4793 -44.6195 -4.2123 REMARK 3 T TENSOR REMARK 3 T11: 0.4175 T22: 0.1689 REMARK 3 T33: 0.2943 T12: -0.0432 REMARK 3 T13: 0.0258 T23: 0.0130 REMARK 3 L TENSOR REMARK 3 L11: 4.1344 L22: 5.8463 REMARK 3 L33: 2.8358 L12: -2.9744 REMARK 3 L13: 1.6022 L23: -2.2053 REMARK 3 S TENSOR REMARK 3 S11: -0.2802 S12: -0.3751 S13: -0.4461 REMARK 3 S21: 0.2289 S22: 0.2384 S23: 0.4746 REMARK 3 S31: 0.2740 S32: -0.2379 S33: 0.0417 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 283 A 337 REMARK 3 ORIGIN FOR THE GROUP (A): 0.8111 -46.8847 -10.6860 REMARK 3 T TENSOR REMARK 3 T11: 0.5357 T22: 0.1850 REMARK 3 T33: 0.2430 T12: -0.0440 REMARK 3 T13: -0.0404 T23: 0.0069 REMARK 3 L TENSOR REMARK 3 L11: 4.9698 L22: 7.7729 REMARK 3 L33: 3.1051 L12: -3.8261 REMARK 3 L13: 0.5055 L23: -1.2237 REMARK 3 S TENSOR REMARK 3 S11: -0.0558 S12: 0.0486 S13: -0.4702 REMARK 3 S21: -0.6259 S22: -0.1061 S23: 0.3156 REMARK 3 S31: 0.7025 S32: 0.2341 S33: 0.1619 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 USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 3VVC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-AUG-12. REMARK 100 THE DEPOSITION ID IS D_1000095545. 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 : 7.5 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-NE3A 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 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.9 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20104 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 80.270 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09600 REMARK 200 FOR THE DATA SET : 9.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.54100 REMARK 200 R SYM FOR SHELL (I) : 0.54100 REMARK 200 FOR SHELL : 1.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.1.4 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HEPES-NAOH, PEG 400, AMMONIUM SULFATE, REMARK 280 PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 80.27000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 46.34391 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 26.68333 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 80.27000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 46.34391 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 26.68333 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 80.27000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 46.34391 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 26.68333 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 80.27000 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 46.34391 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 26.68333 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 80.27000 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 46.34391 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 26.68333 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 80.27000 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 46.34391 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 26.68333 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 92.68781 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 53.36667 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 92.68781 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 53.36667 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 92.68781 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 53.36667 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 92.68781 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 53.36667 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 92.68781 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 53.36667 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 92.68781 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 53.36667 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 29080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 73000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -555.0 KCAL/MOL 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 4 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 5 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 S SO4 A 406 LIES ON A SPECIAL POSITION. REMARK 375 O3 SO4 A 406 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 561 LIES ON A SPECIAL POSITION. 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 -20 REMARK 465 ASN A -19 REMARK 465 HIS A -18 REMARK 465 LYS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 SER A -10 REMARK 465 SER A -9 REMARK 465 GLY A -8 REMARK 465 LEU A -7 REMARK 465 VAL A -6 REMARK 465 PRO A -5 REMARK 465 ARG A -4 REMARK 465 GLY A -3 REMARK 465 SER A -2 REMARK 465 ALA A -1 REMARK 465 SER A 285 REMARK 465 ARG A 286 REMARK 465 ASP A 287 REMARK 465 LEU A 288 REMARK 465 ASN A 289 REMARK 465 TYR A 290 REMARK 465 SER A 291 REMARK 465 ASN A 292 REMARK 465 TYR A 293 REMARK 465 VAL A 294 REMARK 465 GLU A 295 REMARK 465 THR A 296 REMARK 465 GLY A 297 REMARK 465 ASN A 298 REMARK 465 GLU A 299 REMARK 465 LYS A 300 REMARK 465 ILE A 301 REMARK 465 THR A 302 REMARK 465 GLN A 303 REMARK 465 SER A 304 REMARK 465 LYS A 338 REMARK 465 ALA A 339 REMARK 465 SER A 340 REMARK 465 MET A 341 REMARK 465 ARG A 342 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 LYS A 183 CG CD CE NZ REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG A 254 CB CG CD NE CZ NH1 NH2 REMARK 480 HIS A 255 CB CG ND1 CD2 CE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 TYR A 76 CB TYR A 76 CG 0.104 REMARK 500 ARG A 254 CA ARG A 254 CB -0.132 REMARK 500 HIS A 255 CA HIS A 255 CB -0.226 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 LEU A 122 CA - CB - CG ANGL. DEV. = 14.0 DEGREES REMARK 500 ARG A 150 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A 254 CB - CA - C ANGL. DEV. = 16.3 DEGREES REMARK 500 HIS A 255 CB - CA - C ANGL. DEV. = -31.3 DEGREES REMARK 500 HIS A 255 N - CA - CB ANGL. DEV. = 12.2 DEGREES REMARK 500 HIS A 255 CA - CB - CG ANGL. DEV. = -17.1 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 ASP A 3 114.80 -39.98 REMARK 500 ASP A 26 27.62 -78.63 REMARK 500 SER A 27 -162.39 -101.94 REMARK 500 ASN A 50 48.58 38.62 REMARK 500 ASP A 73 4.93 80.44 REMARK 500 ILE A 101 -62.44 -104.36 REMARK 500 GLN A 156 -85.75 -75.32 REMARK 500 GLN A 156 -85.75 -77.58 REMARK 500 THR A 191 -71.29 -96.05 REMARK 500 GLU A 243 51.81 39.19 REMARK 500 HIS A 255 90.01 -63.17 REMARK 500 ASN A 311 42.92 -104.37 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 NAP A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 406 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4G5H RELATED DB: PDB REMARK 900 CAPE COMPLEXED WITH UDP-GLCNAC REMARK 900 RELATED ID: 3VVB RELATED DB: PDB REMARK 900 CAPE IN APO FORM DBREF 3VVC A 2 342 UNP Q7A2Y4 Q7A2Y4_STAAM 2 342 SEQADV 3VVC MET A -20 UNP Q7A2Y4 EXPRESSION TAG SEQADV 3VVC ASN A -19 UNP Q7A2Y4 EXPRESSION TAG SEQADV 3VVC HIS A -18 UNP Q7A2Y4 EXPRESSION TAG SEQADV 3VVC LYS A -17 UNP Q7A2Y4 EXPRESSION TAG SEQADV 3VVC HIS A -16 UNP Q7A2Y4 EXPRESSION TAG SEQADV 3VVC HIS A -15 UNP Q7A2Y4 EXPRESSION TAG SEQADV 3VVC HIS A -14 UNP Q7A2Y4 EXPRESSION TAG SEQADV 3VVC HIS A -13 UNP Q7A2Y4 EXPRESSION TAG SEQADV 3VVC HIS A -12 UNP Q7A2Y4 EXPRESSION TAG SEQADV 3VVC HIS A -11 UNP Q7A2Y4 EXPRESSION TAG SEQADV 3VVC SER A -10 UNP Q7A2Y4 EXPRESSION TAG SEQADV 3VVC SER A -9 UNP Q7A2Y4 EXPRESSION TAG SEQADV 3VVC GLY A -8 UNP Q7A2Y4 EXPRESSION TAG SEQADV 3VVC LEU A -7 UNP Q7A2Y4 EXPRESSION TAG SEQADV 3VVC VAL A -6 UNP Q7A2Y4 EXPRESSION TAG SEQADV 3VVC PRO A -5 UNP Q7A2Y4 EXPRESSION TAG SEQADV 3VVC ARG A -4 UNP Q7A2Y4 EXPRESSION TAG SEQADV 3VVC GLY A -3 UNP Q7A2Y4 EXPRESSION TAG SEQADV 3VVC SER A -2 UNP Q7A2Y4 EXPRESSION TAG SEQADV 3VVC ALA A -1 UNP Q7A2Y4 EXPRESSION TAG SEQADV 3VVC MET A 0 UNP Q7A2Y4 EXPRESSION TAG SEQADV 3VVC GLY A 1 UNP Q7A2Y4 EXPRESSION TAG SEQADV 3VVC GLU A 126 UNP Q7A2Y4 LYS 126 ENGINEERED MUTATION SEQRES 1 A 363 MET ASN HIS LYS HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 363 LEU VAL PRO ARG GLY SER ALA MET GLY PHE ASP ASP LYS SEQRES 3 A 363 ILE LEU LEU ILE THR GLY GLY THR GLY SER PHE GLY ASN SEQRES 4 A 363 ALA VAL MET LYS ARG PHE LEU ASP SER ASN ILE LYS GLU SEQRES 5 A 363 ILE ARG ILE PHE SER ARG ASP GLU LYS LYS GLN ASP ASP SEQRES 6 A 363 ILE ARG LYS LYS TYR ASN ASN SER LYS LEU LYS PHE TYR SEQRES 7 A 363 ILE GLY ASP VAL ARG ASP SER GLN SER VAL GLU THR ALA SEQRES 8 A 363 MET ARG ASP VAL ASP TYR VAL PHE HIS ALA ALA ALA LEU SEQRES 9 A 363 LYS GLN VAL PRO SER CYS GLU PHE PHE PRO VAL GLU ALA SEQRES 10 A 363 VAL LYS THR ASN ILE ILE GLY THR GLU ASN VAL LEU GLN SEQRES 11 A 363 SER ALA ILE HIS GLN ASN VAL LYS LYS VAL ILE CYS LEU SEQRES 12 A 363 SER THR ASP GLU ALA ALA TYR PRO ILE ASN ALA MET GLY SEQRES 13 A 363 ILE SER LYS ALA MET MET GLU LYS VAL PHE VAL ALA LYS SEQRES 14 A 363 SER ARG ASN ILE ARG SER GLU GLN THR LEU ILE CYS GLY SEQRES 15 A 363 THR ARG TYR GLY ASN VAL MET ALA SER ARG GLY SER VAL SEQRES 16 A 363 ILE PRO LEU PHE ILE ASP LYS ILE LYS ALA GLY GLU PRO SEQRES 17 A 363 LEU THR ILE THR ASP PRO ASP MET THR ARG PHE LEU MET SEQRES 18 A 363 SER LEU GLU ASP ALA VAL GLU LEU VAL VAL HIS ALA PHE SEQRES 19 A 363 LYS HIS ALA GLU THR GLY ASP ILE MET VAL GLN LYS ALA SEQRES 20 A 363 PRO SER SER THR VAL GLY ASP LEU ALA THR ALA LEU LEU SEQRES 21 A 363 GLU LEU PHE GLU ALA ASP ASN ALA ILE GLU ILE ILE GLY SEQRES 22 A 363 THR ARG HIS GLY GLU LYS LYS ALA GLU THR LEU LEU THR SEQRES 23 A 363 ARG GLU GLU TYR ALA GLN CYS GLU ASP MET GLY ASP TYR SEQRES 24 A 363 PHE ARG VAL PRO ALA ASP SER ARG ASP LEU ASN TYR SER SEQRES 25 A 363 ASN TYR VAL GLU THR GLY ASN GLU LYS ILE THR GLN SER SEQRES 26 A 363 TYR GLU TYR ASN SER ASP ASN THR HIS ILE LEU THR VAL SEQRES 27 A 363 GLU GLU ILE LYS GLU LYS LEU LEU THR LEU GLU TYR VAL SEQRES 28 A 363 ARG ASN GLU LEU ASN ASP TYR LYS ALA SER MET ARG HET NAP A 401 48 HET SO4 A 402 5 HET SO4 A 403 5 HET SO4 A 404 5 HET SO4 A 405 5 HET SO4 A 406 5 HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETNAM SO4 SULFATE ION HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE FORMUL 2 NAP C21 H28 N7 O17 P3 FORMUL 3 SO4 5(O4 S 2-) FORMUL 8 HOH *82(H2 O) HELIX 1 1 GLY A 14 LEU A 25 1 12 HELIX 2 2 ASP A 38 ASN A 50 1 13 HELIX 3 3 ASP A 63 ARG A 72 1 10 HELIX 4 4 GLN A 85 PHE A 92 1 8 HELIX 5 5 PHE A 92 ILE A 101 1 10 HELIX 6 6 ILE A 101 GLN A 114 1 14 HELIX 7 7 GLU A 126 ALA A 128 5 3 HELIX 8 8 ASN A 132 ILE A 152 1 21 HELIX 9 9 VAL A 174 GLY A 185 1 12 HELIX 10 10 SER A 201 ALA A 216 1 16 HELIX 11 11 VAL A 231 PHE A 242 1 12 HELIX 12 12 THR A 265 CYS A 272 1 8 HELIX 13 13 THR A 316 THR A 326 1 11 HELIX 14 14 LEU A 327 TYR A 337 1 11 SHEET 1 A 9 LEU A 54 ILE A 58 0 SHEET 2 A 9 GLU A 31 SER A 36 1 N ILE A 32 O LYS A 55 SHEET 3 A 9 ILE A 6 THR A 10 1 N LEU A 7 O ARG A 33 SHEET 4 A 9 TYR A 76 HIS A 79 1 O PHE A 78 N LEU A 8 SHEET 5 A 9 LYS A 118 THR A 124 1 O ILE A 120 N HIS A 79 SHEET 6 A 9 LEU A 158 TYR A 164 1 O CYS A 160 N CYS A 121 SHEET 7 A 9 ILE A 221 GLN A 224 1 O MET A 222 N GLY A 161 SHEET 8 A 9 TYR A 278 VAL A 281 -1 O VAL A 281 N ILE A 221 SHEET 9 A 9 GLU A 273 ASP A 274 -1 N GLU A 273 O ARG A 280 SHEET 1 B 2 LEU A 188 ILE A 190 0 SHEET 2 B 2 ILE A 248 ILE A 250 1 O GLU A 249 N LEU A 188 SHEET 1 C 2 THR A 196 PHE A 198 0 SHEET 2 C 2 SER A 228 THR A 230 -1 O SER A 229 N ARG A 197 SHEET 1 D 2 THR A 262 LEU A 264 0 SHEET 2 D 2 TYR A 307 ASN A 308 -1 O TYR A 307 N LEU A 264 CISPEP 1 MET A 0 GLY A 1 0 21.28 SITE 1 AC1 28 GLY A 11 THR A 13 GLY A 14 SER A 15 SITE 2 AC1 28 PHE A 16 SER A 36 ARG A 37 ASP A 38 SITE 3 AC1 28 LYS A 40 LYS A 41 ASP A 60 VAL A 61 SITE 4 AC1 28 ARG A 62 ALA A 80 ALA A 81 ALA A 82 SITE 5 AC1 28 LYS A 84 SER A 123 THR A 124 LYS A 138 SITE 6 AC1 28 TYR A 164 GLY A 165 HOH A 526 HOH A 541 SITE 7 AC1 28 HOH A 542 HOH A 561 HOH A 571 HOH A 576 SITE 1 AC2 4 ILE A 152 ARG A 153 SER A 154 HOH A 546 SITE 1 AC3 4 LEU A 202 GLU A 203 LEU A 327 GLU A 328 SITE 1 AC4 4 ARG A 72 HIS A 113 GLN A 114 SO4 A 406 SITE 1 AC5 3 HIS A 211 LYS A 214 HIS A 215 SITE 1 AC6 2 HIS A 113 SO4 A 404 CRYST1 160.540 160.540 80.050 90.00 90.00 120.00 H 3 2 18 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 0.006229 0.003596 0.000000 0.00000 SCALE2 0.000000 0.007193 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012492 0.00000