PDB Short entry for 1OQW HEADER CELL ADHESION 11-MAR-03 1OQW TITLE FULL-LENGTH PAK PILIN FROM PSEUDOMONAS AERUGINOSA COMPND MOL_ID: 1; COMPND 2 MOLECULE: FIMBRIAL PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PILIN, STRAIN PAK SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA; SOURCE 3 ORGANISM_TAXID: 287; SOURCE 4 STRAIN: K KEYWDS TYPE IV PILIN, FIBER-FORMING PROTEIN, ADHESION, PSEUDOMONAS KEYWDS 2 AERUGIONOSA, PAK PILIN, CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR L.CRAIG,A.S.ARVAI,K.T.FOREST,J.A.TAINER REVDAT 3 16-AUG-23 1OQW 1 REMARK REVDAT 2 24-FEB-09 1OQW 1 VERSN REVDAT 1 03-JUN-03 1OQW 0 JRNL AUTH L.CRAIG,R.K.TAYLOR,M.E.PIQUE,B.A.ADAIR,A.S.ARVAI,M.SINGH, JRNL AUTH 2 S.J.LLOYD,D.S.SHIN,E.D.GETZOFF,M.YEAGER,K.T.FOREST, JRNL AUTH 3 J.A.TAINER JRNL TITL TYPE IV PILIN STRUCTURE AND ASSEMBLY: X-RAY AND EM ANALYSES JRNL TITL 2 OF VIBRIO CHOLERAE TOXIN-COREGULATED PILUS AND PSEUDOMONAS JRNL TITL 3 AERUGINOSA PAK PILIN JRNL REF MOL.CELL V. 11 1139 2003 JRNL REFN ISSN 1097-2765 JRNL PMID 12769840 JRNL DOI 10.1016/S1097-2765(03)00170-9 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.9 REMARK 3 NUMBER OF REFLECTIONS : 27307 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : USED THROUGHOUT REFINEMENT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.223 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1322 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.30 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2800 REMARK 3 BIN FREE R VALUE : 0.2800 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 42 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 : 2106 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 282 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.86000 REMARK 3 B22 (A**2) : -1.06200 REMARK 3 B33 (A**2) : -3.79800 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.12000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 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) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1OQW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-MAR-03. REMARK 100 THE DEPOSITION ID IS D_1000018580. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUN-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 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) : 0.9791 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28468 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.700 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 3.240 REMARK 200 R MERGE (I) : 0.07900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.28 REMARK 200 R MERGE FOR SHELL (I) : 0.33000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: AMORE REMARK 200 STARTING MODEL: 1DZO.PDB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% MPD, 35% PEG 4000, 100 MM SODIUM REMARK 280 CITRATE, 2.5 MM MNCL2, PH 5.6, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 73.50750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.21100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 73.50750 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.21100 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 300 REMARK: THOUSANDS OF PILIN SUBUNITS ASSEMBLE TO FORM A LONG THIN REMARK 300 FILAMENT ~8 NM IN DIAMETER AND SEVERAL MICRONS IN LENGTH 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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: 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 LYS A 81 -3.26 -58.89 REMARK 500 LYS B 81 -7.50 -55.46 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1OQV RELATED DB: PDB REMARK 900 STRUCTURE OF THE TYPE IV PILIN SUBUNIT FROM THE TOXIN CO-REGULATED REMARK 900 PILUS OF VIBRIO CHOLERAE CLASSICAL BIOTYPE REMARK 900 RELATED ID: 1OR9 RELATED DB: PDB REMARK 900 MODEL FOR ASSEMBLY OF THE VIBRIO CHOLERAE TOXIN CO-REGULATED PILUS REMARK 900 (TCP) BASED ON EM AND X-RAY CRYSTALLOGRAPHY REMARK 900 RELATED ID: 1DZO RELATED DB: PDB REMARK 900 TRUNCATED PAK PILIN FROM PSEUDOMONAS AERUGINOSA REMARK 900 RELATED ID: 2PIL RELATED DB: PDB REMARK 900 CRYSTALLOGRAPHIC STRUCTURE OF PHOSPHORYLATED PILIN FROM NEISSERIA DBREF 1OQW A 1 144 UNP P02973 FMPA_PSEAE 7 150 DBREF 1OQW B 1 144 UNP P02973 FMPA_PSEAE 7 150 SEQRES 1 A 144 PHE THR LEU ILE GLU LEU MET ILE VAL VAL ALA ILE ILE SEQRES 2 A 144 GLY ILE LEU ALA ALA ILE ALA ILE PRO GLN TYR GLN ASN SEQRES 3 A 144 TYR VAL ALA ARG SER GLU GLY ALA SER ALA LEU ALA SER SEQRES 4 A 144 VAL ASN PRO LEU LYS THR THR VAL GLU GLU ALA LEU SER SEQRES 5 A 144 ARG GLY TRP SER VAL LYS SER GLY THR GLY THR GLU ASP SEQRES 6 A 144 ALA THR LYS LYS GLU VAL PRO LEU GLY VAL ALA ALA ASP SEQRES 7 A 144 ALA ASN LYS LEU GLY THR ILE ALA LEU LYS PRO ASP PRO SEQRES 8 A 144 ALA ASP GLY THR ALA ASP ILE THR LEU THR PHE THR MET SEQRES 9 A 144 GLY GLY ALA GLY PRO LYS ASN LYS GLY LYS ILE ILE THR SEQRES 10 A 144 LEU THR ARG THR ALA ALA ASP GLY LEU TRP LYS CYS THR SEQRES 11 A 144 SER ASP GLN ASP GLU GLN PHE ILE PRO LYS GLY CYS SER SEQRES 12 A 144 ARG SEQRES 1 B 144 PHE THR LEU ILE GLU LEU MET ILE VAL VAL ALA ILE ILE SEQRES 2 B 144 GLY ILE LEU ALA ALA ILE ALA ILE PRO GLN TYR GLN ASN SEQRES 3 B 144 TYR VAL ALA ARG SER GLU GLY ALA SER ALA LEU ALA SER SEQRES 4 B 144 VAL ASN PRO LEU LYS THR THR VAL GLU GLU ALA LEU SER SEQRES 5 B 144 ARG GLY TRP SER VAL LYS SER GLY THR GLY THR GLU ASP SEQRES 6 B 144 ALA THR LYS LYS GLU VAL PRO LEU GLY VAL ALA ALA ASP SEQRES 7 B 144 ALA ASN LYS LEU GLY THR ILE ALA LEU LYS PRO ASP PRO SEQRES 8 B 144 ALA ASP GLY THR ALA ASP ILE THR LEU THR PHE THR MET SEQRES 9 B 144 GLY GLY ALA GLY PRO LYS ASN LYS GLY LYS ILE ILE THR SEQRES 10 B 144 LEU THR ARG THR ALA ALA ASP GLY LEU TRP LYS CYS THR SEQRES 11 B 144 SER ASP GLN ASP GLU GLN PHE ILE PRO LYS GLY CYS SER SEQRES 12 B 144 ARG FORMUL 3 HOH *282(H2 O) HELIX 1 1 THR A 2 ASN A 41 1 40 HELIX 2 2 PRO A 42 SER A 52 1 11 HELIX 3 3 ASP A 134 ILE A 138 5 5 HELIX 4 4 THR B 2 ASN B 41 1 40 HELIX 5 5 PRO B 42 ARG B 53 1 12 HELIX 6 6 ASP B 134 ILE B 138 5 5 SHEET 1 A 2 SER A 56 LYS A 58 0 SHEET 2 A 2 GLU A 70 PRO A 72 1 O VAL A 71 N LYS A 58 SHEET 1 B 4 THR A 84 LYS A 88 0 SHEET 2 B 4 ILE A 98 THR A 103 -1 O THR A 99 N LYS A 88 SHEET 3 B 4 ILE A 115 ARG A 120 -1 O ARG A 120 N ILE A 98 SHEET 4 B 4 TRP A 127 SER A 131 -1 O THR A 130 N THR A 117 SHEET 1 C 2 SER B 56 LYS B 58 0 SHEET 2 C 2 GLU B 70 PRO B 72 1 O VAL B 71 N LYS B 58 SHEET 1 D 4 THR B 84 LYS B 88 0 SHEET 2 D 4 ILE B 98 THR B 103 -1 O THR B 99 N LYS B 88 SHEET 3 D 4 ILE B 115 ARG B 120 -1 O ARG B 120 N ILE B 98 SHEET 4 D 4 TRP B 127 SER B 131 -1 O THR B 130 N THR B 117 SSBOND 1 CYS A 129 CYS A 142 1555 1555 2.04 SSBOND 2 CYS B 129 CYS B 142 1555 1555 2.04 CISPEP 1 LYS A 88 PRO A 89 0 -0.76 CISPEP 2 ASP A 90 PRO A 91 0 0.06 CISPEP 3 LYS B 88 PRO B 89 0 -0.62 CISPEP 4 ASP B 90 PRO B 91 0 0.39 CRYST1 147.015 44.422 73.782 90.00 116.82 90.00 C 1 2 1 8 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 0.006802 0.000000 0.003439 0.00000 SCALE2 0.000000 0.022511 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015187 0.00000