HEADER TOXIN 21-AUG-19 6U3F TITLE STRUCTURE-BASED DISCOVERY OF A NOVEL SMALL-MOLECULE INHIBITOR OF TITLE 2 METHICILLIN-RESISTANT S. AUREUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PANTON-VALENTINE LEUCOCIDIN F; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 25-325; COMPND 5 SYNONYM: PANTON-VALENTINE LEUKOCIDIN CHAIN F,PANTON-VALENTINE COMPND 6 LEUKOCIDIN CHAIN F PROTEIN,PANTON-VALENTINE LEUKOCIDIN F; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 GENE: LUKF-PV, HLGB_1, LUKF- PV, LUKPV-F, LUKPV-F, LUKPVF, SOURCE 5 NCTC6133_01921; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI K-12; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 83333 KEYWDS ALPHA-TOXIN, PVL, LEUKOCIDINS, MRSA, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR J.LIU,L.KOZHAYA,V.J.TORRES,D.UNUTMAZ,M.LU REVDAT 4 11-OCT-23 6U3F 1 REMARK REVDAT 3 13-MAY-20 6U3F 1 JRNL REVDAT 2 01-APR-20 6U3F 1 JRNL REVDAT 1 25-MAR-20 6U3F 0 JRNL AUTH J.LIU,L.KOZHAYA,V.J.TORRES,D.UNUTMAZ,M.LU JRNL TITL STRUCTURE-BASED DISCOVERY OF A SMALL-MOLECULE INHIBITOR OF JRNL TITL 2 METHICILLIN-RESISTANTSTAPHYLOCOCCUS AUREUSVIRULENCE. JRNL REF J.BIOL.CHEM. V. 295 5944 2020 JRNL REFN ESSN 1083-351X JRNL PMID 32179646 JRNL DOI 10.1074/JBC.RA120.012697 REMARK 2 REMARK 2 RESOLUTION. 1.78 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0238 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.78 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.49 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 35471 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) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1887 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) : 1.78 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.83 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2520 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.86 REMARK 3 BIN R VALUE (WORKING SET) : 0.1540 REMARK 3 BIN FREE R VALUE SET COUNT : 166 REMARK 3 BIN FREE R VALUE : 0.1950 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2389 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 35 REMARK 3 SOLVENT ATOMS : 192 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.86 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.67000 REMARK 3 B22 (A**2) : 0.67000 REMARK 3 B33 (A**2) : -2.17000 REMARK 3 B12 (A**2) : 0.33000 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): 0.104 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.103 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.061 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.796 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.951 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2475 ; 0.017 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3347 ; 2.438 ; 1.654 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 291 ; 6.964 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 137 ;38.013 ;24.234 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 432 ;16.027 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;10.500 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 319 ; 0.203 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1893 ; 0.017 ; 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 : 1 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 1 A 301 REMARK 3 ORIGIN FOR THE GROUP (A): 13.4060 45.8320 278.7220 REMARK 3 T TENSOR REMARK 3 T11: 0.0201 T22: 0.0509 REMARK 3 T33: 0.0094 T12: 0.0116 REMARK 3 T13: -0.0067 T23: 0.0104 REMARK 3 L TENSOR REMARK 3 L11: 0.1561 L22: 0.2097 REMARK 3 L33: 1.3897 L12: 0.1536 REMARK 3 L13: 0.0267 L23: -0.1420 REMARK 3 S TENSOR REMARK 3 S11: 0.0193 S12: -0.0168 S13: -0.0176 REMARK 3 S21: 0.0093 S22: -0.0100 S23: 0.0002 REMARK 3 S31: -0.0068 S32: 0.1165 S33: -0.0093 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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: U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 6U3F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-AUG-19. REMARK 100 THE DEPOSITION ID IS D_1000243837. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-NOV-18 REMARK 200 TEMPERATURE (KELVIN) : 100 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 : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37358 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.780 REMARK 200 RESOLUTION RANGE LOW (A) : 89.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 9.400 REMARK 200 R MERGE (I) : 0.03500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.78 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.82 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : 9.20 REMARK 200 R MERGE FOR SHELL (I) : 0.10900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 20.00 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: PDB ENTRY 1PVL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10 MG/ML PROTEIN IN 10 MM SODIUM REMARK 280 ACETATE, PH 5.4, 10 MM FOS-CHOLINE 14, 30 MM BETA-OG AGAINST REMARK 280 RESERVOIR SOLUTION OF 2.6 M AMMONIUM SULFATE, 5% PEG400, 0.1 M REMARK 280 HEPES, PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-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 177.91133 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 88.95567 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 88.95567 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 177.91133 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 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 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 129 REMARK 465 GLY A 130 REMARK 465 GLY A 131 REMARK 465 GLY A 132 REMARK 465 ASN A 133 REMARK 465 GLY A 134 REMARK 465 SER A 135 REMARK 465 LYS A 136 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 O1 SO4 A 404 O HOH A 501 2.11 REMARK 500 NE2 GLN A 104 NH2 ARG A 150 2.18 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 660 O HOH A 660 5677 2.02 REMARK 500 O HOH A 635 O HOH A 635 5677 2.13 REMARK 500 O HOH A 623 O HOH A 656 4457 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 GLU A 106 CD GLU A 106 OE2 0.104 REMARK 500 GLU A 140 CD GLU A 140 OE2 0.073 REMARK 500 GLU A 269 CD GLU A 269 OE2 -0.090 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 TYR A 82 CB - CG - CD1 ANGL. DEV. = -4.0 DEGREES REMARK 500 ASN A 87 CB - CA - C ANGL. DEV. = 13.9 DEGREES REMARK 500 ASN A 87 CA - CB - CG ANGL. DEV. = -13.2 DEGREES REMARK 500 ASN A 105 CB - CA - C ANGL. DEV. = 12.2 DEGREES REMARK 500 ARG A 150 CD - NE - CZ ANGL. DEV. = 9.1 DEGREES REMARK 500 ARG A 150 NE - CZ - NH1 ANGL. DEV. = 6.1 DEGREES REMARK 500 ARG A 251 NE - CZ - NH1 ANGL. DEV. = -3.2 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 13 -150.62 -167.72 REMARK 500 ALA A 56 -163.24 -128.03 REMARK 500 THR A 71 -76.08 -86.57 REMARK 500 ASN A 91 109.60 -166.04 REMARK 500 ASN A 103 -125.75 74.86 REMARK 500 GLN A 146 43.75 -152.17 REMARK 500 SER A 148 -8.24 84.71 REMARK 500 HIS A 169 -54.79 -130.81 REMARK 500 ASN A 206 48.17 -99.07 REMARK 500 ALA A 235 -167.19 -105.44 REMARK 500 GLN A 258 -14.43 89.33 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ASN A 87 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 PQJ A 401 REMARK 610 PQJ A 402 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PQJ A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PQJ 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 DBREF 6U3F A 1 301 UNP Q5FBD2 Q5FBD2_STAAU 25 325 SEQRES 1 A 301 ALA GLN HIS ILE THR PRO VAL SER GLU LYS LYS VAL ASP SEQRES 2 A 301 ASP LYS ILE THR LEU TYR LYS THR THR ALA THR SER ASP SEQRES 3 A 301 SER ASP LYS LEU LYS ILE SER GLN ILE LEU THR PHE ASN SEQRES 4 A 301 PHE ILE LYS ASP LYS SER TYR ASP LYS ASP THR LEU ILE SEQRES 5 A 301 LEU LYS ALA ALA GLY ASN ILE TYR SER GLY TYR THR LYS SEQRES 6 A 301 PRO ASN PRO LYS ASP THR ILE SER SER GLN PHE TYR TRP SEQRES 7 A 301 GLY SER LYS TYR ASN ILE SER ILE ASN SER ASP SER ASN SEQRES 8 A 301 ASP SER VAL ASN VAL VAL ASP TYR ALA PRO LYS ASN GLN SEQRES 9 A 301 ASN GLU GLU PHE GLN VAL GLN GLN THR VAL GLY TYR SER SEQRES 10 A 301 TYR GLY GLY ASP ILE ASN ILE SER ASN GLY LEU SER GLY SEQRES 11 A 301 GLY GLY ASN GLY SER LYS SER PHE SER GLU THR ILE ASN SEQRES 12 A 301 TYR LYS GLN GLU SER TYR ARG THR SER LEU ASP LYS ARG SEQRES 13 A 301 THR ASN PHE LYS LYS ILE GLY TRP ASP VAL GLU ALA HIS SEQRES 14 A 301 LYS ILE MET ASN ASN GLY TRP GLY PRO TYR GLY ARG ASP SEQRES 15 A 301 SER TYR HIS SER THR TYR GLY ASN GLU MET PHE LEU GLY SEQRES 16 A 301 SER ARG GLN SER ASN LEU ASN ALA GLY GLN ASN PHE LEU SEQRES 17 A 301 GLU TYR HIS LYS MET PRO VAL LEU SER ARG GLY ASN PHE SEQRES 18 A 301 ASN PRO GLU PHE ILE GLY VAL LEU SER ARG LYS GLN ASN SEQRES 19 A 301 ALA ALA LYS LYS SER LYS ILE THR VAL THR TYR GLN ARG SEQRES 20 A 301 GLU MET ASP ARG TYR THR ASN PHE TRP ASN GLN LEU HIS SEQRES 21 A 301 TRP ILE GLY ASN ASN TYR LYS ASP GLU ASN ARG ALA THR SEQRES 22 A 301 HIS THR SER ILE TYR GLU VAL ASP TRP GLU ASN HIS THR SEQRES 23 A 301 VAL LYS LEU ILE ASP THR GLN SER LYS GLU LYS ASN PRO SEQRES 24 A 301 MET SER HET PQJ A 401 12 HET PQJ A 402 13 HET SO4 A 403 5 HET SO4 A 404 5 HETNAM PQJ FOS-CHOLINE-14 HETNAM SO4 SULFATE ION HETSYN PQJ TETRADECYL 2-(TRIMETHYL-$L^{4}-AZANYL)ETHYL HYDROGEN HETSYN 2 PQJ PHOSPHATE FORMUL 2 PQJ 2(C19 H43 N O4 P) FORMUL 4 SO4 2(O4 S 2-) FORMUL 6 HOH *192(H2 O) HELIX 1 AA1 ASN A 202 ASN A 206 5 5 HELIX 2 AA2 GLU A 209 MET A 213 5 5 HELIX 3 AA3 PRO A 214 GLY A 219 1 6 SHEET 1 AA1 6 GLN A 2 ILE A 4 0 SHEET 2 AA1 6 ILE A 16 SER A 27 -1 O THR A 24 N HIS A 3 SHEET 3 AA1 6 ILE A 32 ASP A 43 -1 O PHE A 38 N THR A 21 SHEET 4 AA1 6 LYS A 48 TYR A 60 -1 O THR A 50 N ILE A 41 SHEET 5 AA1 6 PHE A 225 LYS A 232 -1 O PHE A 225 N ALA A 55 SHEET 6 AA1 6 VAL A 94 ALA A 100 -1 N ASP A 98 O VAL A 228 SHEET 1 AA2 5 SER A 8 LYS A 11 0 SHEET 2 AA2 5 ILE A 16 SER A 27 -1 O LEU A 18 N LYS A 10 SHEET 3 AA2 5 ILE A 32 ASP A 43 -1 O PHE A 38 N THR A 21 SHEET 4 AA2 5 LYS A 48 TYR A 60 -1 O THR A 50 N ILE A 41 SHEET 5 AA2 5 ASN A 220 PHE A 221 -1 O PHE A 221 N ILE A 59 SHEET 1 AA3 7 GLN A 104 ASN A 105 0 SHEET 2 AA3 7 TYR A 149 LEU A 153 -1 O THR A 151 N ASN A 105 SHEET 3 AA3 7 LYS A 161 ALA A 168 -1 O ASP A 165 N SER A 152 SHEET 4 AA3 7 SER A 73 ASP A 89 -1 N ILE A 86 O ILE A 162 SHEET 5 AA3 7 LYS A 238 TRP A 256 -1 O GLU A 248 N LYS A 81 SHEET 6 AA3 7 TRP A 261 ASP A 281 -1 O VAL A 280 N SER A 239 SHEET 7 AA3 7 THR A 286 GLU A 296 -1 O LYS A 288 N GLU A 279 SHEET 1 AA4 3 ASP A 121 ASN A 126 0 SHEET 2 AA4 3 GLN A 109 SER A 117 -1 N GLY A 115 O ASN A 123 SHEET 3 AA4 3 PHE A 138 LYS A 145 -1 O GLU A 140 N VAL A 114 SHEET 1 AA5 2 ILE A 171 ASN A 173 0 SHEET 2 AA5 2 TRP A 176 TYR A 179 -1 O TRP A 176 N ASN A 173 CISPEP 1 ALA A 100 PRO A 101 0 -1.60 CISPEP 2 GLY A 177 PRO A 178 0 13.01 SITE 1 AC1 8 ASN A 173 TRP A 176 TYR A 179 GLU A 191 SITE 2 AC1 8 LEU A 194 GLY A 195 SER A 196 ARG A 197 SITE 1 AC2 5 THR A 71 SER A 199 ASN A 200 LEU A 201 SITE 2 AC2 5 ASN A 202 SITE 1 AC3 4 HIS A 185 ARG A 197 LYS A 295 HOH A 607 SITE 1 AC4 8 TYR A 210 VAL A 215 ARG A 218 GLY A 219 SITE 2 AC4 8 ASN A 220 HOH A 501 HOH A 508 HOH A 647 CRYST1 49.249 49.249 266.867 90.00 90.00 120.00 P 32 2 1 6 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 0.020305 0.011723 0.000000 0.00000 SCALE2 0.000000 0.023446 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003747 0.00000