HEADER TRANSPORT PROTEIN 21-OCT-15 5FL3 TITLE PILT2 FROM THERMUS THERMOPHILUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PILI RETRACTION PROTEIN PILT; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PILT2; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 274; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSPORT PROTEIN, ATPASE EXPDTA X-RAY DIFFRACTION AUTHOR V.KARUPPIAH,J.P.DERRICK REVDAT 2 10-JAN-24 5FL3 1 REMARK REVDAT 1 11-NOV-15 5FL3 0 JRNL AUTH V.KARUPPIAH,J.P.DERRICK JRNL TITL PILT2 FROM THERMUS THERMOPHILUS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.52 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.52 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 15770 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 779 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 42.7671 - 4.5779 1.00 2533 141 0.1517 0.1772 REMARK 3 2 4.5779 - 3.6342 1.00 2510 128 0.1531 0.2304 REMARK 3 3 3.6342 - 3.1750 1.00 2511 125 0.2102 0.2901 REMARK 3 4 3.1750 - 2.8848 1.00 2467 120 0.2309 0.3079 REMARK 3 5 2.8848 - 2.6780 1.00 2492 121 0.2391 0.3362 REMARK 3 6 2.6780 - 2.5202 1.00 2478 144 0.2527 0.3465 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.380 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 44.26 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 : 0.009 2870 REMARK 3 ANGLE : 1.279 3887 REMARK 3 CHIRALITY : 0.046 455 REMARK 3 PLANARITY : 0.006 493 REMARK 3 DIHEDRAL : 15.904 1097 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 5FL3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-OCT-15. REMARK 100 THE DEPOSITION ID IS D_1290065335. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-APR-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.900 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15793 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.520 REMARK 200 RESOLUTION RANGE LOW (A) : 42.760 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.400 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.52 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : 0.76000 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: PDB ENTRY 2EWV REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS/HCL PH 5.5, 1%(W/V) PEG REMARK 280 3350, 1.0 M AMMONIUM SULFATE REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 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 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 47.63333 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 23.81667 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 35.72500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 11.90833 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 59.54167 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 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 MET A 1 REMARK 465 SER A 2 REMARK 465 GLU A 3 REMARK 465 ALA A 4 REMARK 465 GLN A 5 REMARK 465 GLY A 6 REMARK 465 GLN A 7 REMARK 465 GLY A 8 REMARK 465 LYS A 9 REMARK 465 THR A 364 REMARK 465 GLY A 365 REMARK 465 GLN A 366 REMARK 465 THR A 367 REMARK 465 TYR A 368 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 ARG A 23 33.36 72.75 REMARK 500 VAL A 87 -59.66 -127.35 REMARK 500 LYS A 179 -102.70 -125.03 REMARK 500 LEU A 190 -57.04 -126.97 REMARK 500 GLN A 285 48.90 -90.02 REMARK 500 GLN A 312 11.69 -63.79 REMARK 500 ARG A 326 151.23 176.85 REMARK 500 LYS A 362 38.34 -84.53 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 ADP A 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 402 DBREF 5FL3 A 1 368 UNP Q5SHF6 Q5SHF6_THET8 1 368 SEQADV 5FL3 THR A 310 UNP Q5SHF6 MET 310 CONFLICT SEQRES 1 A 368 MET SER GLU ALA GLN GLY GLN GLY LYS GLN SER LEU VAL SEQRES 2 A 368 GLU MET LEU LYS ALA MET VAL GLN ALA ARG ALA SER ASP SEQRES 3 A 368 ILE HIS LEU GLN ALA GLY ALA PRO PRO THR VAL ARG ILE SEQRES 4 A 368 ASP GLY LYS LEU ARG PRO PHE GLY ASN ARG PRO LEU THR SEQRES 5 A 368 PRO LYS GLU VAL GLU ALA ILE ALA ARG ALA LEU LEU THR SEQRES 6 A 368 PRO GLU GLN LEU GLU GLU LEU GLU TYR ARG LYS GLU MET SEQRES 7 A 368 ASP PHE ALA TYR THR ILE PRO GLY VAL ALA ARG PHE ARG SEQRES 8 A 368 CYS ASN LEU LEU ARG GLN ARG GLY SER PHE GLY LEU VAL SEQRES 9 A 368 MET ARG VAL VAL SER GLU VAL ILE PRO SER PHE GLU ALA SEQRES 10 A 368 LEU GLY LEU PRO ARG GLU VAL MET GLU SER LEU ALA ALA SEQRES 11 A 368 LYS GLU ARG GLY LEU ILE LEU VAL THR GLY PRO THR GLY SEQRES 12 A 368 SER GLY LYS SER THR THR LEU ALA ALA LEU ILE ASP HIS SEQRES 13 A 368 ILE ASN LEU HIS TYR ALA LYS ASN ILE ILE THR ILE GLU SEQRES 14 A 368 ASP PRO ILE GLU PHE LEU HIS LYS HIS LYS LYS SER LEU SEQRES 15 A 368 VAL VAL GLN ARG GLU VAL GLY LEU ASP THR ASP SER PHE SEQRES 16 A 368 TYR THR GLY LEU LYS TYR ALA LEU ARG GLN ASP PRO ASP SEQRES 17 A 368 VAL ILE MET VAL GLY GLU MET ARG ASP ARG GLU THR VAL SEQRES 18 A 368 GLU ALA ALA LEU MET ALA ALA GLN THR GLY HIS LEU VAL SEQRES 19 A 368 LEU SER THR LEU HIS THR LEU ASP ALA TRP ARG THR ILE SEQRES 20 A 368 ASN ARG ILE ILE ASP PHE PHE PRO LEU HIS GLU HIS ARG SEQRES 21 A 368 GLN VAL ARG VAL LEU LEU ALA GLU SER LEU LEU GLY ILE SEQRES 22 A 368 LEU SER GLN ARG LEU LEU PRO LYS ALA ASP GLY GLN GLY SEQRES 23 A 368 ARG VAL LEU ALA LEU GLU ILE LEU ILE ALA THR PRO TYR SEQRES 24 A 368 VAL ARG GLU LEU LEU LYS ASP GLU GLU LYS THR PRO GLN SEQRES 25 A 368 ILE LYS GLU ALA MET MET GLU GLY SER LEU TYR GLY MET SEQRES 26 A 368 ARG THR PHE ASP GLN HIS LEU VAL GLU LEU TYR THR GLU SEQRES 27 A 368 GLY LEU ILE SER LEU GLU ASP ALA LEU SER ALA ALA THR SEQRES 28 A 368 SER PRO HIS GLU PHE ARG LEU LEU LEU THR LYS ALA THR SEQRES 29 A 368 GLY GLN THR TYR HET ADP A 400 27 HET GOL A 401 6 HET CL A 402 1 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM GOL GLYCEROL HETNAM CL CHLORIDE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 ADP C10 H15 N5 O10 P2 FORMUL 3 GOL C3 H8 O3 FORMUL 4 CL CL 1- FORMUL 5 HOH *45(H2 O) HELIX 1 1 GLN A 10 ALA A 22 1 13 HELIX 2 2 THR A 52 LEU A 64 1 13 HELIX 3 3 THR A 65 GLU A 73 1 9 HELIX 4 4 SER A 114 GLY A 119 1 6 HELIX 5 5 PRO A 121 LYS A 131 1 11 HELIX 6 6 GLY A 145 TYR A 161 1 17 HELIX 7 7 SER A 194 LEU A 203 1 10 HELIX 8 8 ASP A 217 GLY A 231 1 15 HELIX 9 9 ASP A 242 ASP A 252 1 11 HELIX 10 10 PRO A 255 HIS A 257 5 3 HELIX 11 11 GLU A 258 SER A 269 1 12 HELIX 12 12 THR A 297 ASP A 306 1 10 HELIX 13 13 LYS A 309 PRO A 311 5 3 HELIX 14 14 GLN A 312 GLU A 319 1 8 HELIX 15 15 THR A 327 GLU A 338 1 12 HELIX 16 16 SER A 342 ALA A 350 1 9 HELIX 17 17 SER A 352 LYS A 362 1 11 SHEET 1 AA 6 LYS A 42 PRO A 45 0 SHEET 2 AA 6 THR A 36 ILE A 39 -1 O VAL A 37 N ARG A 44 SHEET 3 AA 6 ASP A 26 GLN A 30 -1 O ASP A 26 N ARG A 38 SHEET 4 AA 6 SER A 100 VAL A 108 -1 O LEU A 103 N LEU A 29 SHEET 5 AA 6 ALA A 88 GLN A 97 -1 O ARG A 89 N VAL A 108 SHEET 6 AA 6 MET A 78 ILE A 84 -1 O MET A 78 N LEU A 94 SHEET 1 AB 7 LEU A 182 GLU A 187 0 SHEET 2 AB 7 ASN A 164 GLU A 169 1 O ILE A 165 N VAL A 184 SHEET 3 AB 7 VAL A 209 VAL A 212 1 O VAL A 209 N ILE A 166 SHEET 4 AB 7 LEU A 233 LEU A 238 1 O LEU A 233 N ILE A 210 SHEET 5 AB 7 GLY A 134 THR A 139 1 O GLY A 134 N VAL A 234 SHEET 6 AB 7 LEU A 270 PRO A 280 1 N LEU A 271 O LEU A 135 SHEET 7 AB 7 ARG A 287 ILE A 295 -1 O VAL A 288 N LEU A 279 CISPEP 1 ASP A 170 PRO A 171 0 -3.36 CISPEP 2 TYR A 323 GLY A 324 0 -24.34 SITE 1 AC1 12 LEU A 118 GLY A 143 SER A 144 GLY A 145 SITE 2 AC1 12 LYS A 146 SER A 147 THR A 148 LEU A 278 SITE 3 AC1 12 ARG A 287 HOH A2021 HOH A2023 HOH A2025 SITE 1 AC2 7 PRO A 113 SER A 114 PHE A 115 ARG A 122 SITE 2 AC2 7 ALA A 152 ASP A 155 HIS A 156 SITE 1 AC3 2 ALA A 31 GLN A 97 CRYST1 106.750 106.750 71.450 90.00 90.00 120.00 P 65 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 0.009368 0.005408 0.000000 0.00000 SCALE2 0.000000 0.010817 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013996 0.00000