HEADER STRUCTURAL PROTEIN 22-SEP-09 3JYZ TITLE CRYSTAL STRUCTURE OF PSEUDOMONAS AERUGINOSA (STRAIN: TITLE 2 PA110594) TYPEIV PILIN IN SPACE GROUP P41212 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYPE IV PILIN STRUCTURAL SUBUNIT; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 34-178; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA; SOURCE 3 ORGANISM_TAXID: 287; SOURCE 4 STRAIN: PA110594; SOURCE 5 GENE: PILA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: D-TOPO-PET151 KEYWDS PILA, METHYLATION, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.NGUYEN,S.G.JACKSON,F.AIDOO,M.S.JUNOP,L.L.BURROWS REVDAT 2 16-FEB-10 3JYZ 1 JRNL REVDAT 1 24-NOV-09 3JYZ 0 JRNL AUTH Y.NGUYEN,S.G.JACKSON,F.AIDOO,M.JUNOP,L.L.BURROWS JRNL TITL STRUCTURAL CHARACTERIZATION OF NOVEL PSEUDOMONAS JRNL TITL 2 AERUGINOSA TYPE IV PILINS. JRNL REF J.MOL.BIOL. V. 395 491 2010 JRNL REFN ISSN 0022-2836 JRNL PMID 19895819 JRNL DOI 10.1016/J.JMB.2009.10.070 REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : MLHL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.84 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 20149 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.820 REMARK 3 FREE R VALUE TEST SET COUNT : 1978 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 29.8424 - 3.7349 0.99 1430 158 0.1743 0.1950 REMARK 3 2 3.7349 - 2.9653 1.00 1360 143 0.1797 0.1701 REMARK 3 3 2.9653 - 2.5907 1.00 1329 153 0.1795 0.1927 REMARK 3 4 2.5907 - 2.3540 1.00 1312 139 0.1798 0.2170 REMARK 3 5 2.3540 - 2.1853 0.99 1306 142 0.1729 0.2124 REMARK 3 6 2.1853 - 2.0565 0.98 1276 140 0.1633 0.2068 REMARK 3 7 2.0565 - 1.9535 0.97 1271 135 0.1644 0.2182 REMARK 3 8 1.9535 - 1.8685 0.99 1284 130 0.1837 0.2566 REMARK 3 9 1.8685 - 1.7966 0.97 1244 145 0.1687 0.2378 REMARK 3 10 1.7966 - 1.7346 0.99 1266 144 0.1467 0.1914 REMARK 3 11 1.7346 - 1.6804 0.99 1281 141 0.1464 0.2239 REMARK 3 12 1.6804 - 1.6323 0.99 1279 138 0.1374 0.2042 REMARK 3 13 1.6323 - 1.5894 0.99 1279 129 0.1347 0.2050 REMARK 3 14 1.5894 - 1.5500 0.98 1254 141 0.1422 0.1895 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.36 REMARK 3 B_SOL : 52.96 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.019 1119 REMARK 3 ANGLE : 1.391 1527 REMARK 3 CHIRALITY : 0.082 190 REMARK 3 PLANARITY : 0.007 201 REMARK 3 DIHEDRAL : 15.893 380 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3JYZ COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-SEP-09. REMARK 100 THE RCSB ID CODE IS RCSB055336. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JUN-09 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 : NSLS REMARK 200 BEAMLINE : X12C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9800 REMARK 200 MONOCHROMATOR : DOUBLE-CRYSTAL SI(111) REMARK 200 OPTICS : BEAM FOCUSED BY A TOROIDAL REMARK 200 MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20404 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 14.500 REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 33.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-HCL PH 8.5, 2.0 M REMARK 280 AMMONIUM SULFATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 33.86800 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 31.52950 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 31.52950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 16.93400 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 31.52950 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 31.52950 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 50.80200 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 31.52950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 31.52950 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 16.93400 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 31.52950 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 31.52950 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 50.80200 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 33.86800 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 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 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 HOH A 317 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 272 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 357 LIES ON A SPECIAL POSITION. REMARK 375 S SO4 A 201 LIES ON A SPECIAL POSITION. 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 SER A 143 -150.35 -113.37 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 SO4 A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DZO RELATED DB: PDB REMARK 900 PSEUDOMONAS AERUGINOSA PAK TYPEIV A REMARK 900 RELATED ID: 1QVE RELATED DB: PDB REMARK 900 PSEUDOMONAS AERUGINOSA K122-4 TYPEIV A REMARK 900 RELATED ID: 1A2Y RELATED DB: PDB REMARK 900 NEISSERIA GONORRHOEAE MS11 TYPEIV A REMARK 900 RELATED ID: 1Q5F RELATED DB: PDB REMARK 900 SALMONELLA TYPHI TYPEIV B REMARK 900 RELATED ID: 1ZWT RELATED DB: PDB REMARK 900 ENTEROPHATHOGENIC ESCHERICHIA COLI E2348/69 TYPEIV B REMARK 900 RELATED ID: 1OQV RELATED DB: PDB REMARK 900 VIBRIO CHOLERAE RT4236 TYPEIV B DBREF 3JYZ A 28 172 UNP Q8KQ36 Q8KQ36_PSEAE 34 178 SEQADV 3JYZ GLY A 23 UNP Q8KQ36 EXPRESSION TAG SEQADV 3JYZ ILE A 24 UNP Q8KQ36 EXPRESSION TAG SEQADV 3JYZ ASP A 25 UNP Q8KQ36 EXPRESSION TAG SEQADV 3JYZ PRO A 26 UNP Q8KQ36 EXPRESSION TAG SEQADV 3JYZ PHE A 27 UNP Q8KQ36 EXPRESSION TAG SEQRES 1 A 150 GLY ILE ASP PRO PHE THR VAL ARG THR ARG VAL SER GLU SEQRES 2 A 150 GLY LEU VAL LEU ALA GLU PRO ALA LYS LEU MSE ILE SER SEQRES 3 A 150 THR ASP GLY SER ALA SER THR ALA ASP LEU THR ARG ALA SEQRES 4 A 150 THR THR THR TRP ASN GLN GLN SER ASN ASN LEU GLY ALA SEQRES 5 A 150 SER SER LYS TYR VAL THR SER VAL LEU MSE ASP ALA GLY SEQRES 6 A 150 ASN THR GLY VAL ILE THR ILE THR TYR VAL ALA ASP GLN SEQRES 7 A 150 VAL GLY LEU PRO THR ALA GLY ASN THR LEU ILE LEU SER SEQRES 8 A 150 PRO TYR ILE ASN ASP GLY ASN THR ARG THR ALA LEU ALA SEQRES 9 A 150 THR ALA VAL ALA ALA GLY THR ARG GLY THR ILE ASP TRP SEQRES 10 A 150 ALA CYS THR SER ALA SER ASN ALA THR ALA THR ALA GLN SEQRES 11 A 150 GLY PHE THR GLY MSE ALA ALA GLY SER VAL PRO GLN GLU SEQRES 12 A 150 PHE ALA PRO ALA GLN CYS ARG MODRES 3JYZ MSE A 46 MET SELENOMETHIONINE MODRES 3JYZ MSE A 84 MET SELENOMETHIONINE MODRES 3JYZ MSE A 157 MET SELENOMETHIONINE HET MSE A 46 8 HET MSE A 84 8 HET MSE A 157 8 HET SO4 A 201 5 HETNAM MSE SELENOMETHIONINE HETNAM SO4 SULFATE ION FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 2 SO4 O4 S 2- FORMUL 3 HOH *256(H2 O) HELIX 1 1 ASP A 25 GLY A 51 1 27 HELIX 2 2 SER A 54 LEU A 72 1 19 HELIX 3 3 VAL A 97 GLY A 102 1 6 HELIX 4 4 LEU A 125 GLY A 132 1 8 HELIX 5 5 ASN A 146 GLN A 152 1 7 HELIX 6 6 PRO A 163 ALA A 167 5 5 HELIX 7 7 PRO A 168 ARG A 172 5 5 SHEET 1 A 4 VAL A 79 MSE A 84 0 SHEET 2 A 4 ILE A 92 TYR A 96 -1 O THR A 93 N LEU A 83 SHEET 3 A 4 THR A 109 ASN A 117 -1 O LEU A 112 N ILE A 92 SHEET 4 A 4 ARG A 122 ALA A 124 -1 O THR A 123 N ILE A 116 SHEET 1 B 4 VAL A 79 MSE A 84 0 SHEET 2 B 4 ILE A 92 TYR A 96 -1 O THR A 93 N LEU A 83 SHEET 3 B 4 THR A 109 ASN A 117 -1 O LEU A 112 N ILE A 92 SHEET 4 B 4 THR A 136 THR A 142 -1 O THR A 136 N ASN A 117 SSBOND 1 CYS A 141 CYS A 171 1555 1555 2.04 LINK C LEU A 45 N MSE A 46 1555 1555 1.34 LINK C MSE A 46 N ILE A 47 1555 1555 1.33 LINK C LEU A 83 N MSE A 84 1555 1555 1.33 LINK C MSE A 84 N ASP A 85 1555 1555 1.32 LINK C GLY A 156 N MSE A 157 1555 1555 1.33 LINK C MSE A 157 N ALA A 158 1555 1555 1.33 SITE 1 AC1 6 ARG A 30 PRO A 168 ALA A 169 ARG A 172 SITE 2 AC1 6 HOH A 284 HOH A 376 CRYST1 63.059 63.059 67.736 90.00 90.00 90.00 P 41 21 2 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 0.015858 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015858 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014763 0.00000