PDB Short entry for 1IO1 HEADER STRUCTURAL PROTEIN 28-DEC-00 1IO1 TITLE CRYSTAL STRUCTURE OF F41 FRAGMENT OF FLAGELLIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHASE 1 FLAGELLIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: F41 L-TYPE (RESIDUES 54-451); COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SALMONELLA TYPHIMURIUM; SOURCE 3 ORGANISM_TAXID: 602; SOURCE 4 STRAIN: SJW 1660; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BETA-FOLIUM, FLAGELLIN, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR F.A.SAMATEY,K.IMADA,S.NAGASHIMA,F.VONDERVISZ,T.KUMASAKA,M.YAMAMOTO, AUTHOR 2 K.NAMBA REVDAT 4 27-DEC-23 1IO1 1 SEQADV REVDAT 3 24-FEB-09 1IO1 1 VERSN REVDAT 2 15-APR-03 1IO1 1 SOURCE DBREF SEQADV REVDAT 1 04-APR-01 1IO1 0 JRNL AUTH F.A.SAMATEY,K.IMADA,S.NAGASHIMA,F.VONDERVISZ,T.KUMASAKA, JRNL AUTH 2 M.YAMAMOTO,K.NAMBA JRNL TITL STRUCTURE OF THE BACTERIAL FLAGELLAR PROTOFILAMENT AND JRNL TITL 2 IMPLICATIONS FOR A SWITCH FOR SUPERCOILING JRNL REF NATURE V. 410 331 2001 JRNL REFN ISSN 0028-0836 JRNL PMID 11268201 JRNL DOI 10.1038/35066504 REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 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) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 29866 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) : 0.234 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 2467 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 : 2880 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 354 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.47 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) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.523 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 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 1IO1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-JAN-01. REMARK 100 THE DEPOSITION ID IS D_1000005108. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-NOV-99 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.931 REMARK 200 MONOCHROMATOR : DIAMOND 111 + GERMANIUM 220 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA, CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 121314 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 31.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.27200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 6000, NACL, GLYCEROL, ISO REMARK 280 -PROPANOL, PH 7.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 18.22000 REMARK 290 SMTRY3 2 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 PHE A 53 REMARK 465 THR A 54 REMARK 465 ALA A 55 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 O HOH A 655 O HOH A 677 1.70 REMARK 500 OD1 ASN A 82 O HOH A 846 1.76 REMARK 500 O SER A 205 O HOH A 849 1.79 REMARK 500 OG SER A 310 O HOH A 854 1.93 REMARK 500 OE1 GLN A 89 O HOH A 848 1.94 REMARK 500 O HOH A 563 O HOH A 609 1.95 REMARK 500 O HOH A 826 O HOH A 846 1.97 REMARK 500 O HOH A 603 O HOH A 607 2.00 REMARK 500 OE1 GLU A 114 O HOH A 847 2.00 REMARK 500 O HOH A 659 O HOH A 667 2.01 REMARK 500 OH TYR A 230 O HOH A 851 2.03 REMARK 500 O HOH A 546 O HOH A 677 2.09 REMARK 500 O HOH A 565 O HOH A 724 2.09 REMARK 500 O HOH A 744 O HOH A 754 2.12 REMARK 500 O HOH A 589 O HOH A 677 2.15 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 THR A 193 -160.04 -104.15 REMARK 500 LEU A 197 104.18 -55.47 REMARK 500 ASP A 224 8.07 -69.36 REMARK 500 LYS A 251 3.55 -65.57 REMARK 500 THR A 252 -63.76 -107.12 REMARK 500 LYS A 348 106.40 72.21 REMARK 500 ALA A 351 -167.52 51.61 REMARK 500 ASP A 352 -46.19 168.32 REMARK 500 ASP A 353 44.91 -162.17 REMARK 500 THR A 355 160.67 88.35 REMARK 500 GLN A 393 78.07 -151.54 REMARK 500 PRO A 394 -136.15 -75.65 REMARK 500 ASP A 395 103.64 29.12 REMARK 500 GLU A 398 -168.34 -70.79 REMARK 500 ALA A 449 156.58 165.16 REMARK 500 REMARK 500 REMARK: NULL DBREF 1IO1 A 53 450 UNP P06179 FLIC_SALTY 53 450 SEQADV 1IO1 ALA A 426 UNP P06179 GLY 426 CONFLICT SEQRES 1 A 398 PHE THR ALA ASN ILE LYS GLY LEU THR GLN ALA SER ARG SEQRES 2 A 398 ASN ALA ASN ASP GLY ILE SER ILE ALA GLN THR THR GLU SEQRES 3 A 398 GLY ALA LEU ASN GLU ILE ASN ASN ASN LEU GLN ARG VAL SEQRES 4 A 398 ARG GLU LEU ALA VAL GLN SER ALA ASN SER THR ASN SER SEQRES 5 A 398 GLN SER ASP LEU ASP SER ILE GLN ALA GLU ILE THR GLN SEQRES 6 A 398 ARG LEU ASN GLU ILE ASP ARG VAL SER GLY GLN THR GLN SEQRES 7 A 398 PHE ASN GLY VAL LYS VAL LEU ALA GLN ASP ASN THR LEU SEQRES 8 A 398 THR ILE GLN VAL GLY ALA ASN ASP GLY GLU THR ILE ASP SEQRES 9 A 398 ILE ASP LEU LYS GLN ILE ASN SER GLN THR LEU GLY LEU SEQRES 10 A 398 ASP THR LEU ASN VAL GLN GLN LYS TYR LYS VAL SER ASP SEQRES 11 A 398 THR ALA ALA THR VAL THR GLY TYR ALA ASP THR THR ILE SEQRES 12 A 398 ALA LEU ASP ASN SER THR PHE LYS ALA SER ALA THR GLY SEQRES 13 A 398 LEU GLY GLY THR ASP GLN LYS ILE ASP GLY ASP LEU LYS SEQRES 14 A 398 PHE ASP ASP THR THR GLY LYS TYR TYR ALA LYS VAL THR SEQRES 15 A 398 VAL THR GLY GLY THR GLY LYS ASP GLY TYR TYR GLU VAL SEQRES 16 A 398 SER VAL ASP LYS THR ASN GLY GLU VAL THR LEU ALA GLY SEQRES 17 A 398 GLY ALA THR SER PRO LEU THR GLY GLY LEU PRO ALA THR SEQRES 18 A 398 ALA THR GLU ASP VAL LYS ASN VAL GLN VAL ALA ASN ALA SEQRES 19 A 398 ASP LEU THR GLU ALA LYS ALA ALA LEU THR ALA ALA GLY SEQRES 20 A 398 VAL THR GLY THR ALA SER VAL VAL LYS MET SER TYR THR SEQRES 21 A 398 ASP ASN ASN GLY LYS THR ILE ASP GLY GLY LEU ALA VAL SEQRES 22 A 398 LYS VAL GLY ASP ASP TYR TYR SER ALA THR GLN ASN LYS SEQRES 23 A 398 ASP GLY SER ILE SER ILE ASN THR THR LYS TYR THR ALA SEQRES 24 A 398 ASP ASP GLY THR SER LYS THR ALA LEU ASN LYS LEU GLY SEQRES 25 A 398 GLY ALA ASP GLY LYS THR GLU VAL VAL SER ILE GLY GLY SEQRES 26 A 398 LYS THR TYR ALA ALA SER LYS ALA GLU GLY HIS ASN PHE SEQRES 27 A 398 LYS ALA GLN PRO ASP LEU ALA GLU ALA ALA ALA THR THR SEQRES 28 A 398 THR GLU ASN PRO LEU GLN LYS ILE ASP ALA ALA LEU ALA SEQRES 29 A 398 GLN VAL ASP THR LEU ARG SER ASP LEU ALA ALA VAL GLN SEQRES 30 A 398 ASN ARG PHE ASN SER ALA ILE THR ASN LEU GLY ASN THR SEQRES 31 A 398 VAL ASN ASN LEU THR SER ALA ARG FORMUL 2 HOH *354(H2 O) HELIX 1 1 ILE A 57 ALA A 99 1 43 HELIX 2 2 SER A 104 THR A 129 1 26 HELIX 3 3 ASN A 199 PHE A 202 5 4 HELIX 4 4 ALA A 206 GLY A 210 5 5 HELIX 5 5 LEU A 288 ALA A 298 1 11 HELIX 6 6 ALA A 382 GLU A 386 1 5 HELIX 7 7 ASN A 406 SER A 448 1 43 SHEET 1 A 2 ASN A 141 GLN A 146 0 SHEET 2 A 2 THR A 154 LEU A 159 -1 O ILE A 155 N ILE A 145 SHEET 1 B 5 LYS A 179 ALA A 184 0 SHEET 2 B 5 ALA A 304 THR A 312 -1 N LYS A 308 O THR A 183 SHEET 3 B 5 THR A 318 VAL A 327 -1 O ILE A 319 N TYR A 311 SHEET 4 B 5 ASP A 330 GLN A 336 -1 O ASP A 330 N VAL A 327 SHEET 5 B 5 ILE A 342 ILE A 344 -1 N SER A 343 O THR A 335 SHEET 1 C 2 TYR A 190 ALA A 196 0 SHEET 2 C 2 ASN A 280 ALA A 284 -1 N VAL A 281 O ILE A 195 SHEET 1 D 4 VAL A 256 LEU A 258 0 SHEET 2 D 4 GLY A 243 VAL A 249 -1 N SER A 248 O THR A 257 SHEET 3 D 4 TYR A 229 THR A 236 -1 O TYR A 229 N VAL A 247 SHEET 4 D 4 ASP A 213 ILE A 216 -1 O ASP A 213 N THR A 236 SHEET 1 E 5 VAL A 256 LEU A 258 0 SHEET 2 E 5 GLY A 243 VAL A 249 -1 N SER A 248 O THR A 257 SHEET 3 E 5 TYR A 229 THR A 236 -1 O TYR A 229 N VAL A 247 SHEET 4 E 5 LEU A 220 PHE A 222 -1 O LYS A 221 N TYR A 230 SHEET 5 E 5 GLU A 276 VAL A 278 -1 O GLU A 276 N PHE A 222 SHEET 1 F 3 ASN A 361 GLY A 364 0 SHEET 2 F 3 THR A 370 ILE A 375 -1 O THR A 370 N GLY A 364 SHEET 3 F 3 LYS A 378 ALA A 381 -1 N LYS A 378 O ILE A 375 CRYST1 51.750 36.440 118.350 90.00 91.15 90.00 P 1 21 1 2 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 0.019324 0.000000 0.000388 0.00000 SCALE2 0.000000 0.027442 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008451 0.00000