HEADER TRANSFERASE 25-FEB-15 4YFY TITLE X-RAY STRUCTURE OF THE VIOF N-FORMYLTRANSFERASE FROM PROVIDENCIA TITLE 2 ALCALIFACIENS O30 IN COMPLEX WITH THF AND TDP-QUI4N COMPND MOL_ID: 1; COMPND 2 MOLECULE: VIOF; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 9-252; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PROVIDENCIA ALCALIFACIENS; SOURCE 3 ORGANISM_TAXID: 126385; SOURCE 4 GENE: VIOF; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ROSETTAS2(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-DUET KEYWDS LIPOPOLYSACCHARIDE O-ANTIGEN, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR N.A.GENTHE,J.B.THODEN,M.M.BENNING,H.M.HOLDEN REVDAT 5 27-SEP-23 4YFY 1 SOURCE JRNL REMARK REVDAT 4 03-JUN-15 4YFY 1 JRNL REVDAT 3 01-APR-15 4YFY 1 JRNL REVDAT 2 25-MAR-15 4YFY 1 AUTHOR REVDAT 1 11-MAR-15 4YFY 0 JRNL AUTH N.A.GENTHE,J.B.THODEN,M.M.BENNING,H.M.HOLDEN JRNL TITL MOLECULAR STRUCTURE OF AN N-FORMYLTRANSFERASE FROM JRNL TITL 2 PROVIDENCIA ALCALIFACIENS O30. JRNL REF PROTEIN SCI. V. 24 976 2015 JRNL REFN ESSN 1469-896X JRNL PMID 25752909 JRNL DOI 10.1002/PRO.2675 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 40605 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) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2161 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2908 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.27 REMARK 3 BIN R VALUE (WORKING SET) : 0.2460 REMARK 3 BIN FREE R VALUE SET COUNT : 154 REMARK 3 BIN FREE R VALUE : 0.2720 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3956 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 139 REMARK 3 SOLVENT ATOMS : 448 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.31 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.37000 REMARK 3 B22 (A**2) : 0.37000 REMARK 3 B33 (A**2) : -1.21000 REMARK 3 B12 (A**2) : 0.37000 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): 0.162 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.158 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.116 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.978 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.912 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4185 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3988 ; 0.000 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5673 ; 2.121 ; 1.999 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9212 ; 0.891 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 482 ; 7.013 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 204 ;40.037 ;26.176 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 769 ;14.782 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;23.302 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 629 ; 0.125 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4651 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 939 ; 0.003 ; 0.020 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 REMARK 4 REMARK 4 4YFY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-FEB-15. REMARK 100 THE DEPOSITION ID IS D_1000207391. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUN-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI-FILTER REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER PLATINUM 135 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SAINT REMARK 200 DATA SCALING SOFTWARE : SADABS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42792 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 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 : 5.300 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : 0.05300 REMARK 200 FOR THE DATA SET : 14.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 0.23700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 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: 4YFV REMARK 200 REMARK 200 REMARK: SIX-SIDED STELLATE RODS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 8-10% PEG-8000, 1 M REMARK 280 TETRAMETHYLAMMONIUM CHLORIDE 100 MM HEPES, PH 7.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277K 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 66.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 38.10512 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 53.80000 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 66.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 38.10512 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 53.80000 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 66.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 38.10512 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 53.80000 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 66.00000 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 38.10512 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 53.80000 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 66.00000 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 38.10512 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 53.80000 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 66.00000 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 38.10512 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 53.80000 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 76.21024 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 107.60000 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 76.21024 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 107.60000 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 76.21024 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 107.60000 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 76.21024 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 107.60000 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 76.21024 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 107.60000 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 76.21024 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 107.60000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 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 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 CL CL A 303 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 SER A 242 REMARK 465 GLN A 243 REMARK 465 GLU A 244 REMARK 465 LEU A 245 REMARK 465 GLU A 246 REMARK 465 SER A 247 REMARK 465 ALA A 248 REMARK 465 HIS A 249 REMARK 465 HIS A 250 REMARK 465 HIS A 251 REMARK 465 HIS A 252 REMARK 465 HIS A 253 REMARK 465 HIS A 254 REMARK 465 SER B 242 REMARK 465 GLN B 243 REMARK 465 GLU B 244 REMARK 465 LEU B 245 REMARK 465 GLU B 246 REMARK 465 SER B 247 REMARK 465 ALA B 248 REMARK 465 HIS B 249 REMARK 465 HIS B 250 REMARK 465 HIS B 251 REMARK 465 HIS B 252 REMARK 465 HIS B 253 REMARK 465 HIS B 254 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 457 O HOH A 467 2.10 REMARK 500 OE2 GLU B 156 O HOH B 401 2.13 REMARK 500 O LEU B 239 O HOH B 402 2.14 REMARK 500 O HOH B 466 O HOH B 602 2.15 REMARK 500 O HOH A 445 O HOH A 466 2.15 REMARK 500 OE1 GLU B 238 O HOH B 519 2.16 REMARK 500 O HOH B 565 O HOH B 597 2.17 REMARK 500 O HOH A 404 O HOH A 453 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 450 O HOH B 436 17555 2.04 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 A 102 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ASP A 201 CB - CG - OD2 ANGL. DEV. = 5.9 DEGREES REMARK 500 ARG A 213 NE - CZ - NH1 ANGL. DEV. = 5.0 DEGREES REMARK 500 ASP A 227 CB - CG - OD1 ANGL. DEV. = 6.4 DEGREES REMARK 500 ARG B 102 NE - CZ - NH2 ANGL. DEV. = 3.9 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 PRO A 95 57.36 -95.13 REMARK 500 ASP A 125 -169.59 -103.37 REMARK 500 HIS A 217 80.36 -155.85 REMARK 500 ASN A 222 -76.22 -111.22 REMARK 500 ASP B 125 -164.45 -109.69 REMARK 500 ASN B 222 -81.47 -114.93 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 0FX A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 1YJ A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 0FX B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 1YJ B 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4YFV RELATED DB: PDB DBREF 4YFY A 1 244 UNP M9P0Q2 M9P0Q2_9ENTR 9 252 DBREF 4YFY B 1 244 UNP M9P0Q2 M9P0Q2_9ENTR 9 252 SEQADV 4YFY LEU A 245 UNP M9P0Q2 EXPRESSION TAG SEQADV 4YFY GLU A 246 UNP M9P0Q2 EXPRESSION TAG SEQADV 4YFY SER A 247 UNP M9P0Q2 EXPRESSION TAG SEQADV 4YFY ALA A 248 UNP M9P0Q2 EXPRESSION TAG SEQADV 4YFY HIS A 249 UNP M9P0Q2 EXPRESSION TAG SEQADV 4YFY HIS A 250 UNP M9P0Q2 EXPRESSION TAG SEQADV 4YFY HIS A 251 UNP M9P0Q2 EXPRESSION TAG SEQADV 4YFY HIS A 252 UNP M9P0Q2 EXPRESSION TAG SEQADV 4YFY HIS A 253 UNP M9P0Q2 EXPRESSION TAG SEQADV 4YFY HIS A 254 UNP M9P0Q2 EXPRESSION TAG SEQADV 4YFY LEU B 245 UNP M9P0Q2 EXPRESSION TAG SEQADV 4YFY GLU B 246 UNP M9P0Q2 EXPRESSION TAG SEQADV 4YFY SER B 247 UNP M9P0Q2 EXPRESSION TAG SEQADV 4YFY ALA B 248 UNP M9P0Q2 EXPRESSION TAG SEQADV 4YFY HIS B 249 UNP M9P0Q2 EXPRESSION TAG SEQADV 4YFY HIS B 250 UNP M9P0Q2 EXPRESSION TAG SEQADV 4YFY HIS B 251 UNP M9P0Q2 EXPRESSION TAG SEQADV 4YFY HIS B 252 UNP M9P0Q2 EXPRESSION TAG SEQADV 4YFY HIS B 253 UNP M9P0Q2 EXPRESSION TAG SEQADV 4YFY HIS B 254 UNP M9P0Q2 EXPRESSION TAG SEQRES 1 A 254 MET LYS LYS ILE LEU VAL ILE SER ASP ASN TYR GLN LEU SEQRES 2 A 254 VAL SER TYR ILE LYS ASN LEU TYR LEU SER ASN GLU GLU SEQRES 3 A 254 TRP SER LYS GLU LEU PHE ILE ASP TYR SER TYR SER SER SEQRES 4 A 254 ILE ASN ARG ASN PRO GLN SER LEU ILE GLU LEU GLY MET SEQRES 5 A 254 THR GLU ILE ASP ILE LYS ASN LYS ASN LEU ASN GLU LEU SEQRES 6 A 254 ASN ASP TYR HIS LEU ILE ILE SER ALA HIS CYS LYS GLN SEQRES 7 A 254 ILE PHE PRO ALA HIS ILE VAL ASN ASN LYS LEU CYS ILE SEQRES 8 A 254 ASN ILE HIS PRO GLY LEU ASN PRO TYR ASN ARG GLY TRP SEQRES 9 A 254 PHE PRO GLN VAL PHE SER ILE LEU ASN LYS LYS PRO ILE SEQRES 10 A 254 GLY ALA THR ILE HIS LYS MET ASP SER GLU VAL ASP HIS SEQRES 11 A 254 GLY GLU ILE TYR CYS GLN GLU GLU VAL SER ILE LEU SER SEQRES 12 A 254 HIS GLU THR SER ILE ASP ILE TYR ASN LYS VAL ILE GLU SEQRES 13 A 254 LEU GLU LYS LYS LEU ILE LYS ASN ASN LEU LEU LYS ILE SEQRES 14 A 254 ILE ASN ASN GLU LEU GLN PRO LYS LEU PRO SER GLN GLU SEQRES 15 A 254 GLY ASN TYR ASN SER ILE GLN ASP PHE ASN LYS LEU CYS SEQRES 16 A 254 LYS LEU ASN LEU GLU ASP ASN GLY SER LEU ARG GLU HIS SEQRES 17 A 254 ILE ASP LEU LEU ARG ALA LEU THR HIS GLY ASP PHE LYS SEQRES 18 A 254 ASN ALA TYR PHE TYR ASP GLU ASN ASN THR LYS VAL PHE SEQRES 19 A 254 VAL LYS ILE GLU LEU SER LEU SER GLN GLU LEU GLU SER SEQRES 20 A 254 ALA HIS HIS HIS HIS HIS HIS SEQRES 1 B 254 MET LYS LYS ILE LEU VAL ILE SER ASP ASN TYR GLN LEU SEQRES 2 B 254 VAL SER TYR ILE LYS ASN LEU TYR LEU SER ASN GLU GLU SEQRES 3 B 254 TRP SER LYS GLU LEU PHE ILE ASP TYR SER TYR SER SER SEQRES 4 B 254 ILE ASN ARG ASN PRO GLN SER LEU ILE GLU LEU GLY MET SEQRES 5 B 254 THR GLU ILE ASP ILE LYS ASN LYS ASN LEU ASN GLU LEU SEQRES 6 B 254 ASN ASP TYR HIS LEU ILE ILE SER ALA HIS CYS LYS GLN SEQRES 7 B 254 ILE PHE PRO ALA HIS ILE VAL ASN ASN LYS LEU CYS ILE SEQRES 8 B 254 ASN ILE HIS PRO GLY LEU ASN PRO TYR ASN ARG GLY TRP SEQRES 9 B 254 PHE PRO GLN VAL PHE SER ILE LEU ASN LYS LYS PRO ILE SEQRES 10 B 254 GLY ALA THR ILE HIS LYS MET ASP SER GLU VAL ASP HIS SEQRES 11 B 254 GLY GLU ILE TYR CYS GLN GLU GLU VAL SER ILE LEU SER SEQRES 12 B 254 HIS GLU THR SER ILE ASP ILE TYR ASN LYS VAL ILE GLU SEQRES 13 B 254 LEU GLU LYS LYS LEU ILE LYS ASN ASN LEU LEU LYS ILE SEQRES 14 B 254 ILE ASN ASN GLU LEU GLN PRO LYS LEU PRO SER GLN GLU SEQRES 15 B 254 GLY ASN TYR ASN SER ILE GLN ASP PHE ASN LYS LEU CYS SEQRES 16 B 254 LYS LEU ASN LEU GLU ASP ASN GLY SER LEU ARG GLU HIS SEQRES 17 B 254 ILE ASP LEU LEU ARG ALA LEU THR HIS GLY ASP PHE LYS SEQRES 18 B 254 ASN ALA TYR PHE TYR ASP GLU ASN ASN THR LYS VAL PHE SEQRES 19 B 254 VAL LYS ILE GLU LEU SER LEU SER GLN GLU LEU GLU SER SEQRES 20 B 254 ALA HIS HIS HIS HIS HIS HIS HET 0FX A 301 35 HET 1YJ A 302 32 HET CL A 303 1 HET EDO A 304 4 HET 0FX B 301 35 HET 1YJ B 302 32 HETNAM 0FX DTDP-4-AMINO-4,6-DIDEOXYGLUCOSE HETNAM 1YJ N-[4-({[(6R)-2-AMINO-4-OXO-3,4,5,6,7,8- HETNAM 2 1YJ HEXAHYDROPTERIDIN-6-YL]METHYL}AMINO)BENZOYL]-L- HETNAM 3 1YJ GLUTAMIC ACID HETNAM CL CHLORIDE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 0FX 2(C16 H27 N3 O14 P2) FORMUL 4 1YJ 2(C19 H23 N7 O6) FORMUL 5 CL CL 1- FORMUL 6 EDO C2 H6 O2 FORMUL 9 HOH *448(H2 O) HELIX 1 AA1 ASN A 10 ASN A 24 1 15 HELIX 2 AA2 ASN A 24 GLU A 30 1 7 HELIX 3 AA3 PRO A 44 GLU A 49 1 6 HELIX 4 AA4 ASN A 61 ASN A 66 5 6 HELIX 5 AA5 PRO A 81 ASN A 86 1 6 HELIX 6 AA6 PHE A 105 LYS A 114 1 10 HELIX 7 AA7 THR A 146 ASN A 171 1 26 HELIX 8 AA8 SER A 187 LYS A 196 1 10 HELIX 9 AA9 LEU A 205 LEU A 215 1 11 HELIX 10 AB1 ASN B 10 ASN B 24 1 15 HELIX 11 AB2 ASN B 24 GLU B 30 1 7 HELIX 12 AB3 PRO B 44 LEU B 50 1 7 HELIX 13 AB4 ASN B 61 ASN B 66 5 6 HELIX 14 AB5 PRO B 81 LYS B 88 1 8 HELIX 15 AB6 PHE B 105 LYS B 114 1 10 HELIX 16 AB7 THR B 146 ASN B 171 1 26 HELIX 17 AB8 SER B 187 LYS B 196 1 10 HELIX 18 AB9 LEU B 205 LEU B 215 1 11 SHEET 1 AA1 7 THR A 53 ILE A 55 0 SHEET 2 AA1 7 LEU A 31 SER A 38 1 N TYR A 37 O ILE A 55 SHEET 3 AA1 7 LYS A 2 SER A 8 1 N ILE A 4 O ASP A 34 SHEET 4 AA1 7 TYR A 68 ALA A 74 1 O ILE A 72 N LEU A 5 SHEET 5 AA1 7 CYS A 90 HIS A 94 1 O ILE A 91 N SER A 73 SHEET 6 AA1 7 ILE A 117 LYS A 123 -1 O HIS A 122 N ASN A 92 SHEET 7 AA1 7 ILE A 133 VAL A 139 -1 O CYS A 135 N ILE A 121 SHEET 1 AA2 2 ARG A 102 GLY A 103 0 SHEET 2 AA2 2 TYR A 185 ASN A 186 1 O ASN A 186 N ARG A 102 SHEET 1 AA3 2 ASN A 202 SER A 204 0 SHEET 2 AA3 2 ASN B 202 SER B 204 -1 O GLY B 203 N GLY A 203 SHEET 1 AA4 4 ALA A 223 TYR A 226 0 SHEET 2 AA4 4 LYS A 232 SER A 240 -1 O VAL A 233 N PHE A 225 SHEET 3 AA4 4 LYS B 232 SER B 240 -1 O LYS B 236 N GLU A 238 SHEET 4 AA4 4 TYR B 224 TYR B 226 -1 N PHE B 225 O VAL B 233 SHEET 1 AA5 7 THR B 53 ILE B 55 0 SHEET 2 AA5 7 LEU B 31 SER B 38 1 N TYR B 37 O ILE B 55 SHEET 3 AA5 7 LYS B 2 SER B 8 1 N VAL B 6 O ASP B 34 SHEET 4 AA5 7 TYR B 68 ALA B 74 1 O HIS B 69 N LYS B 3 SHEET 5 AA5 7 CYS B 90 HIS B 94 1 O ILE B 91 N SER B 73 SHEET 6 AA5 7 ILE B 117 LYS B 123 -1 O THR B 120 N HIS B 94 SHEET 7 AA5 7 ILE B 133 VAL B 139 -1 O TYR B 134 N ILE B 121 SHEET 1 AA6 2 ARG B 102 GLY B 103 0 SHEET 2 AA6 2 TYR B 185 ASN B 186 1 O ASN B 186 N ARG B 102 CISPEP 1 ASN A 98 PRO A 99 0 3.19 CISPEP 2 ASN B 98 PRO B 99 0 3.17 SITE 1 AC1 14 ASN A 10 HIS A 75 LYS A 77 TRP A 104 SITE 2 AC1 14 PHE A 105 GLN A 107 TYR A 151 HIS A 217 SITE 3 AC1 14 PHE A 220 ASN A 222 HOH A 483 HOH A 512 SITE 4 AC1 14 HOH A 523 HOH A 548 SITE 1 AC2 19 SER A 73 CYS A 76 LYS A 77 GLN A 78 SITE 2 AC2 19 ILE A 79 PHE A 80 ASN A 92 TRP A 104 SITE 3 AC2 19 HIS A 122 MET A 124 ASP A 125 GLU A 127 SITE 4 AC2 19 VAL A 128 ASP A 129 TYR A 185 SER A 187 SITE 5 AC2 19 ILE A 188 HOH A 528 HOH A 632 SITE 1 AC3 1 GLN A 181 SITE 1 AC4 6 SER A 143 ARG A 206 ILE A 209 ASP A 210 SITE 2 AC4 6 ARG A 213 PHE B 225 SITE 1 AC5 17 ASN B 10 HIS B 75 LYS B 77 TRP B 104 SITE 2 AC5 17 PHE B 105 GLN B 107 TYR B 151 HIS B 217 SITE 3 AC5 17 PHE B 220 ASN B 222 HOH B 493 HOH B 528 SITE 4 AC5 17 HOH B 557 HOH B 559 HOH B 588 HOH B 600 SITE 5 AC5 17 HOH B 601 SITE 1 AC6 16 SER B 73 CYS B 76 LYS B 77 GLN B 78 SITE 2 AC6 16 ILE B 79 PHE B 80 VAL B 85 ASN B 92 SITE 3 AC6 16 TRP B 104 HIS B 122 MET B 124 ASP B 125 SITE 4 AC6 16 GLU B 127 VAL B 128 ASP B 129 HOH B 489 CRYST1 132.000 132.000 161.400 90.00 90.00 120.00 H 3 2 36 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 0.007576 0.004374 0.000000 0.00000 SCALE2 0.000000 0.008748 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006196 0.00000