HEADER TOXIN 28-JUL-98 2LKF TITLE LEUKOCIDIN F (HLGB) FROM STAPHYLOCOCCUS AUREUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: LEUKOCIDIN F SUBUNIT; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: WATER-SOLUBLE MONOMER; COMPND 5 SYNONYM: LUKF, HLGB; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 STRAIN: SMITH 5R; SOURCE 5 GENE: LUKF; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: DH5A; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PTRCLUKF; SOURCE 10 EXPRESSION_SYSTEM_GENE: LUKF KEYWDS LEUKOTOXIN, HEMOLYSIN, PORE-FORMING TOXIN, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR R.OLSON,H.NARIYA,K.YOKOTA,Y.KAMIO,J.E.GOUAUX REVDAT 4 03-APR-24 2LKF 1 REMARK REVDAT 3 21-FEB-24 2LKF 1 REMARK REVDAT 2 24-FEB-09 2LKF 1 VERSN REVDAT 1 28-JUL-99 2LKF 0 JRNL AUTH R.OLSON,H.NARIYA,K.YOKOTA,Y.KAMIO,E.GOUAUX JRNL TITL CRYSTAL STRUCTURE OF STAPHYLOCOCCAL LUKF DELINEATES JRNL TITL 2 CONFORMATIONAL CHANGES ACCOMPANYING FORMATION OF A JRNL TITL 3 TRANSMEMBRANE CHANNEL. JRNL REF NAT.STRUCT.BIOL. V. 6 134 1999 JRNL REFN ISSN 1072-8368 JRNL PMID 10048924 JRNL DOI 10.1038/5821 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 10622 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.323 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 531 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2380 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 84 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 1.501 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 27.56 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.295 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : PARAM19.SOL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TOPH19.SOL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2LKF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000178317. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : FEB-98 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12697 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.9 REMARK 200 DATA REDUNDANCY : 5.450 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04800 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 54.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.12300 REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR 3.851 REMARK 200 STARTING MODEL: PREVIOUSLY DETERMINED STRUCTURE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 8.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 24.61000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 63.76500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.76000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 63.76500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.61000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.76000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 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 GLU A 1 CG CD OE1 OE2 REMARK 470 ASP A 28 CG OD1 OD2 REMARK 470 ASN A 133 CG OD1 ND2 REMARK 470 ASP A 234 CG OD1 OD2 REMARK 470 LYS A 293 CG CD CE NZ 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 47 32.82 -87.83 REMARK 500 THR A 56 -166.38 -126.61 REMARK 500 SER A 90 164.41 179.75 REMARK 500 ASN A 91 108.28 67.29 REMARK 500 TYR A 99 163.36 176.50 REMARK 500 ASN A 133 153.87 49.19 REMARK 500 GLN A 146 47.90 -148.37 REMARK 500 SER A 148 -3.00 79.32 REMARK 500 ASN A 158 -154.40 -144.81 REMARK 500 ASN A 174 -98.91 -153.78 REMARK 500 SER A 219 -82.90 -119.23 REMARK 500 GLU A 224 99.05 -160.86 REMARK 500 GLN A 233 69.70 -22.40 REMARK 500 ASP A 234 -166.55 -168.07 REMARK 500 ASP A 291 128.55 -173.14 REMARK 500 REMARK 500 REMARK: NULL DBREF 2LKF A 1 299 UNP P0A077 HLGB_STAAU 27 325 SEQRES 1 A 299 GLU GLY LYS ILE THR PRO VAL SER VAL LYS LYS VAL ASP SEQRES 2 A 299 ASP LYS VAL THR LEU TYR LYS THR THR ALA THR ALA ASP SEQRES 3 A 299 SER ASP LYS PHE LYS ILE SER GLN ILE LEU THR PHE ASN SEQRES 4 A 299 PHE ILE LYS ASP LYS SER TYR ASP LYS ASP THR LEU VAL SEQRES 5 A 299 LEU LYS ALA THR GLY ASN ILE ASN SER GLY PHE VAL LYS SEQRES 6 A 299 PRO ASN PRO ASN ASP TYR ASP PHE SER LYS LEU TYR TRP SEQRES 7 A 299 GLY ALA LYS TYR ASN VAL SER ILE SER SER GLN SER ASN SEQRES 8 A 299 ASP SER VAL ASN VAL VAL ASP TYR ALA PRO LYS ASN GLN SEQRES 9 A 299 ASN GLU GLU PHE GLN VAL GLN ASN THR LEU GLY TYR THR SEQRES 10 A 299 PHE GLY GLY ASP ILE SER ILE SER ASN GLY LEU SER GLY SEQRES 11 A 299 GLY LEU ASN GLY ASN THR ALA PHE SER GLU THR ILE ASN SEQRES 12 A 299 TYR LYS GLN GLU SER TYR ARG THR THR LEU SER ARG ASN SEQRES 13 A 299 THR ASN TYR LYS ASN VAL GLY TRP GLY VAL GLU ALA HIS SEQRES 14 A 299 LYS ILE MET ASN ASN GLY TRP GLY PRO TYR GLY ARG ASP SEQRES 15 A 299 SER PHE HIS PRO THR TYR GLY ASN GLU LEU PHE LEU ALA SEQRES 16 A 299 GLY ARG GLN SER SER ALA TYR ALA GLY GLN ASN PHE ILE SEQRES 17 A 299 ALA GLN HIS GLN MET PRO LEU LEU SER ARG SER ASN PHE SEQRES 18 A 299 ASN PRO GLU PHE LEU SER VAL LEU SER HIS ARG GLN ASP SEQRES 19 A 299 GLY ALA LYS LYS SER LYS ILE THR VAL THR TYR GLN ARG SEQRES 20 A 299 GLU MET ASP LEU TYR GLN ILE ARG TRP ASN GLY PHE TYR SEQRES 21 A 299 TRP ALA GLY ALA ASN TYR LYS ASN PHE LYS THR ARG THR SEQRES 22 A 299 PHE LYS SER THR TYR GLU ILE ASP TRP GLU ASN HIS LYS SEQRES 23 A 299 VAL LYS LEU LEU ASP THR LYS GLU THR GLU ASN ASN LYS FORMUL 2 HOH *84(H2 O) HELIX 1 1 ALA A 203 GLN A 205 5 3 HELIX 2 2 GLN A 210 GLN A 212 5 3 HELIX 3 3 LEU A 215 ARG A 218 1 4 SHEET 1 A 6 SER A 8 LYS A 11 0 SHEET 2 A 6 VAL A 16 SER A 27 -1 N LYS A 20 O SER A 8 SHEET 3 A 6 ILE A 32 ASP A 43 -1 N LYS A 42 O THR A 17 SHEET 4 A 6 ASP A 49 ILE A 59 -1 N ASN A 58 O SER A 33 SHEET 5 A 6 PHE A 225 HIS A 231 -1 N HIS A 231 O ASP A 49 SHEET 6 A 6 VAL A 94 ALA A 100 -1 N ALA A 100 O LEU A 226 SHEET 1 B 6 TYR A 149 LEU A 153 0 SHEET 2 B 6 ASN A 161 ALA A 168 -1 N GLU A 167 O ARG A 150 SHEET 3 B 6 PHE A 73 SER A 88 -1 N ILE A 86 O VAL A 162 SHEET 4 B 6 LYS A 238 ARG A 255 -1 N ILE A 254 O SER A 74 SHEET 5 B 6 LYS A 270 ASP A 281 -1 N ILE A 280 O SER A 239 SHEET 6 B 6 LYS A 286 ASN A 298 -1 N ASN A 297 O THR A 271 SHEET 1 C 3 ASP A 121 ASN A 126 0 SHEET 2 C 3 GLN A 109 THR A 117 -1 N THR A 117 O ASP A 121 SHEET 3 C 3 THR A 136 LYS A 145 -1 N TYR A 144 O VAL A 110 SHEET 1 D 2 LEU A 251 TRP A 256 0 SHEET 2 D 2 TRP A 261 TYR A 266 -1 N TYR A 266 O LEU A 251 CISPEP 1 ALA A 100 PRO A 101 0 -0.25 CISPEP 2 GLY A 177 PRO A 178 0 -0.07 CRYST1 49.220 49.520 127.530 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.020317 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020194 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007841 0.00000