PDB Short entry for 3A69 HEADER MOTOR PROTEIN 26-AUG-09 3A69 TITLE ATOMIC MODEL OF THE BACTERIAL FLAGELLAR HOOK BASED ON DOCKING AN X-RAY TITLE 2 DERIVED STRUCTURE AND TERMINAL TWO ALPHA-HELICES INTO AN 7.1 ANGSTROM TITLE 3 RESOLUTION CRYOEM MAP COMPND MOL_ID: 1; COMPND 2 MOLECULE: FLAGELLAR HOOK PROTEIN FLGE; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR SOURCE 3 TYPHIMURIUM; SOURCE 4 ORGANISM_TAXID: 90371; SOURCE 5 STRAIN: SJW880 KEYWDS THE BACTERIAL FLAGELLAR MOTOR, UNIVERSAL JOINT, BACTERIAL FLAGELLUM, KEYWDS 2 MOTOR PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR T.FUJII,T.KATO,K.NAMBA REVDAT 3 13-MAR-24 3A69 1 REMARK REVDAT 2 09-OCT-19 3A69 1 REMARK CRYST1 REVDAT 1 15-DEC-09 3A69 0 JRNL AUTH T.FUJII,T.KATO,K.NAMBA JRNL TITL SPECIFIC ARRANGEMENT OF ALPHA-HELICAL COILED COILS IN THE JRNL TITL 2 CORE DOMAIN OF THE BACTERIAL FLAGELLAR HOOK FOR THE JRNL TITL 3 UNIVERSAL JOINT FUNCTION JRNL REF STRUCTURE V. 17 1485 2009 JRNL REFN ISSN 0969-2126 JRNL PMID 19913483 JRNL DOI 10.1016/J.STR.2009.08.017 REMARK 2 REMARK 2 RESOLUTION. 7.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 7.100 REMARK 3 NUMBER OF PARTICLES : NULL REMARK 3 CTF CORRECTION METHOD : NULL REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: TMV IMAGES REMARK 3 REMARK 3 OTHER DETAILS: A MODIFIED VERSION OF SPIDER PROGRAM WAS USED FOR REMARK 3 THE RECONSTRUCTION REMARK 4 REMARK 4 3A69 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ. REMARK 100 THE DEPOSITION ID IS D_1000028863. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : HELICAL REMARK 245 SPECIMEN TYPE : VITREOUS ICE (CRYO EM) REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : FILAMENT REMARK 245 PARTICLE TYPE : HELICAL REMARK 245 NAME OF SAMPLE : BACTERIAL FLAGELLAR HOOK REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : 20MM TRIS-HCL, 100MM NACL REMARK 245 PH : 7.00 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : 20-FEB-08 REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : 50.00 REMARK 245 MICROSCOPE MODEL : JEOL 3200FSC REMARK 245 DETECTOR TYPE : TVIPS TEMCAM-F415 (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 1.60 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 2000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 50000 REMARK 245 CALIBRATED MAGNIFICATION : 89285 REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 200 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. 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 300 THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR REMARK 300 HELICAL SYMMETRY WITH THE FOLLOWING PARAMETERS: REMARK 300 ROTATION PER SUBUNIT (TWIST) = 64.79 DEGREES REMARK 300 RISE PER SUBUNIT (HEIGHT) = 4.12 ANGSTROMS 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 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 0.808298 -0.588773 0.000000 0.00000 REMARK 350 BIOMT2 1 0.588773 0.808298 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 -20.61500 REMARK 350 BIOMT1 2 -0.188341 -0.982104 0.000000 0.00000 REMARK 350 BIOMT2 2 0.982104 -0.188341 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 -16.49200 REMARK 350 BIOMT1 3 -0.968765 -0.247980 0.000000 0.00000 REMARK 350 BIOMT2 3 0.247980 -0.968765 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 -12.36900 REMARK 350 BIOMT1 4 -0.637047 0.770825 0.000000 0.00000 REMARK 350 BIOMT2 4 -0.770825 -0.637047 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 -8.24600 REMARK 350 BIOMT1 5 0.426000 0.904723 0.000000 0.00000 REMARK 350 BIOMT2 5 -0.904723 0.426000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 -4.12300 REMARK 350 BIOMT1 6 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 6 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 7 0.426000 -0.904723 0.000000 0.00000 REMARK 350 BIOMT2 7 0.904723 0.426000 0.000000 0.00000 REMARK 350 BIOMT3 7 0.000000 0.000000 1.000000 4.12300 REMARK 350 BIOMT1 8 -0.637047 -0.770825 0.000000 0.00000 REMARK 350 BIOMT2 8 0.770825 -0.637047 0.000000 0.00000 REMARK 350 BIOMT3 8 0.000000 0.000000 1.000000 8.24600 REMARK 350 BIOMT1 9 -0.968765 0.247980 0.000000 0.00000 REMARK 350 BIOMT2 9 -0.247980 -0.968765 0.000000 0.00000 REMARK 350 BIOMT3 9 0.000000 0.000000 1.000000 12.36900 REMARK 350 BIOMT1 10 -0.188341 0.982104 0.000000 0.00000 REMARK 350 BIOMT2 10 -0.982104 -0.188341 0.000000 0.00000 REMARK 350 BIOMT3 10 0.000000 0.000000 1.000000 16.49200 REMARK 350 BIOMT1 11 0.808298 0.588773 0.000000 0.00000 REMARK 350 BIOMT2 11 -0.588773 0.808298 0.000000 0.00000 REMARK 350 BIOMT3 11 0.000000 0.000000 1.000000 20.61500 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 ASN A 25 REMARK 465 SER A 26 REMARK 465 ALA A 27 REMARK 465 THR A 28 REMARK 465 TYR A 29 REMARK 465 GLY A 30 REMARK 465 PHE A 31 REMARK 465 LYS A 32 REMARK 465 SER A 33 REMARK 465 GLY A 34 REMARK 465 THR A 35 REMARK 465 ALA A 36 REMARK 465 SER A 37 REMARK 465 PHE A 38 REMARK 465 ALA A 39 REMARK 465 ASP A 40 REMARK 465 MET A 41 REMARK 465 PHE A 42 REMARK 465 ALA A 43 REMARK 465 GLY A 44 REMARK 465 SER A 45 REMARK 465 LYS A 46 REMARK 465 VAL A 47 REMARK 465 GLY A 48 REMARK 465 LEU A 49 REMARK 465 GLY A 50 REMARK 465 VAL A 51 REMARK 465 LYS A 52 REMARK 465 VAL A 53 REMARK 465 ALA A 54 REMARK 465 GLY A 55 REMARK 465 ILE A 56 REMARK 465 THR A 57 REMARK 465 GLN A 58 REMARK 465 ASP A 59 REMARK 465 PHE A 60 REMARK 465 THR A 61 REMARK 465 ASP A 62 REMARK 465 GLY A 63 REMARK 465 THR A 64 REMARK 465 THR A 65 REMARK 465 THR A 66 REMARK 465 ASN A 67 REMARK 465 THR A 68 REMARK 465 GLY A 69 REMARK 465 ARG A 70 REMARK 465 GLY A 358 REMARK 465 ALA A 359 REMARK 465 LEU A 360 REMARK 465 GLU A 361 REMARK 465 ALA A 362 REMARK 465 SER A 363 REMARK 465 ASN A 364 REMARK 465 VAL A 365 REMARK 465 ASP A 366 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 105 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 ARG A 105 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES 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 ASN A 264 -0.53 80.24 REMARK 500 PRO A 285 160.78 -40.68 REMARK 500 ASP A 330 -143.99 48.78 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-1647 RELATED DB: EMDB REMARK 900 7.1 ANGSTROM REOLUTION CRYOEM MAP OF THE BACTERIAL FLAGELLAR HOOK DBREF 3A69 A 1 402 UNP P0A1J1 FLGE_SALTY 2 403 SEQRES 1 A 402 SER PHE SER GLN ALA VAL SER GLY LEU ASN ALA ALA ALA SEQRES 2 A 402 THR ASN LEU ASP VAL ILE GLY ASN ASN ILE ALA ASN SER SEQRES 3 A 402 ALA THR TYR GLY PHE LYS SER GLY THR ALA SER PHE ALA SEQRES 4 A 402 ASP MET PHE ALA GLY SER LYS VAL GLY LEU GLY VAL LYS SEQRES 5 A 402 VAL ALA GLY ILE THR GLN ASP PHE THR ASP GLY THR THR SEQRES 6 A 402 THR ASN THR GLY ARG GLY LEU ASP VAL ALA ILE SER GLN SEQRES 7 A 402 ASN GLY PHE PHE ARG LEU VAL ASP SER ASN GLY SER VAL SEQRES 8 A 402 PHE TYR SER ARG ASN GLY GLN PHE LYS LEU ASP GLU ASN SEQRES 9 A 402 ARG ASN LEU VAL ASN MET GLN GLY MET GLN LEU THR GLY SEQRES 10 A 402 TYR PRO ALA THR GLY THR PRO PRO THR ILE GLN GLN GLY SEQRES 11 A 402 ALA ASN PRO ALA PRO ILE THR ILE PRO ASN THR LEU MET SEQRES 12 A 402 ALA ALA LYS SER THR THR THR ALA SER MET GLN ILE ASN SEQRES 13 A 402 LEU ASN SER THR ASP PRO VAL PRO SER LYS THR PRO PHE SEQRES 14 A 402 SER VAL SER ASP ALA ASP SER TYR ASN LYS LYS GLY THR SEQRES 15 A 402 VAL THR VAL TYR ASP SER GLN GLY ASN ALA HIS ASP MET SEQRES 16 A 402 ASN VAL TYR PHE VAL LYS THR LYS ASP ASN GLU TRP ALA SEQRES 17 A 402 VAL TYR THR HIS ASP SER SER ASP PRO ALA ALA THR ALA SEQRES 18 A 402 PRO THR THR ALA SER THR THR LEU LYS PHE ASN GLU ASN SEQRES 19 A 402 GLY ILE LEU GLU SER GLY GLY THR VAL ASN ILE THR THR SEQRES 20 A 402 GLY THR ILE ASN GLY ALA THR ALA ALA THR PHE SER LEU SEQRES 21 A 402 SER PHE LEU ASN SER MET GLN GLN ASN THR GLY ALA ASN SEQRES 22 A 402 ASN ILE VAL ALA THR ASN GLN ASN GLY TYR LYS PRO GLY SEQRES 23 A 402 ASP LEU VAL SER TYR GLN ILE ASN ASN ASP GLY THR VAL SEQRES 24 A 402 VAL GLY ASN TYR SER ASN GLU GLN GLU GLN VAL LEU GLY SEQRES 25 A 402 GLN ILE VAL LEU ALA ASN PHE ALA ASN ASN GLU GLY LEU SEQRES 26 A 402 ALA SER GLN GLY ASP ASN VAL TRP ALA ALA THR GLN ALA SEQRES 27 A 402 SER GLY VAL ALA LEU LEU GLY THR ALA GLY SER GLY ASN SEQRES 28 A 402 PHE GLY LYS LEU THR ASN GLY ALA LEU GLU ALA SER ASN SEQRES 29 A 402 VAL ASP LEU SER LYS GLU LEU VAL ASN MET ILE VAL ALA SEQRES 30 A 402 GLN ARG ASN TYR GLN SER ASN ALA GLN THR ILE LYS THR SEQRES 31 A 402 GLN ASP GLN ILE LEU ASN THR LEU VAL ASN LEU ARG HELIX 1 1 SER A 1 ALA A 24 1 24 HELIX 2 2 ASN A 321 LEU A 325 5 5 HELIX 3 3 LEU A 367 LEU A 401 1 35 SHEET 1 A 3 LEU A 72 ASP A 73 0 SHEET 2 A 3 GLN A 98 LEU A 101 -1 O PHE A 99 N LEU A 72 SHEET 3 A 3 LEU A 107 VAL A 108 -1 O VAL A 108 N LYS A 100 SHEET 1 B 6 VAL A 91 SER A 94 0 SHEET 2 B 6 PHE A 81 VAL A 85 -1 N LEU A 84 O PHE A 92 SHEET 3 B 6 GLN A 114 PRO A 119 -1 O GLN A 114 N VAL A 85 SHEET 4 B 6 GLU A 308 ILE A 314 -1 O GLN A 313 N TYR A 118 SHEET 5 B 6 THR A 298 TYR A 303 -1 N VAL A 299 O LEU A 311 SHEET 6 B 6 LEU A 288 ILE A 293 -1 N VAL A 289 O ASN A 302 SHEET 1 C 5 ALA A 134 PRO A 135 0 SHEET 2 C 5 GLN A 114 PRO A 119 -1 N GLY A 117 O ALA A 134 SHEET 3 C 5 PHE A 81 VAL A 85 -1 N VAL A 85 O GLN A 114 SHEET 4 C 5 LEU A 316 ASN A 318 -1 O ALA A 317 N PHE A 81 SHEET 5 C 5 LEU A 343 GLY A 345 -1 O GLY A 345 N LEU A 316 SHEET 1 D 4 THR A 242 THR A 246 0 SHEET 2 D 4 THR A 257 SER A 261 -1 O PHE A 258 N ILE A 245 SHEET 3 D 4 THR A 150 ASN A 158 1 N ALA A 151 O SER A 259 SHEET 4 D 4 MET A 266 GLN A 268 1 O MET A 266 N LEU A 157 SHEET 1 E 4 THR A 242 THR A 246 0 SHEET 2 E 4 THR A 257 SER A 261 -1 O PHE A 258 N ILE A 245 SHEET 3 E 4 THR A 150 ASN A 158 1 N ALA A 151 O SER A 259 SHEET 4 E 4 ASN A 274 GLN A 280 -1 O ALA A 277 N GLN A 154 SHEET 1 F 5 LYS A 179 TYR A 186 0 SHEET 2 F 5 ALA A 192 LYS A 203 -1 O HIS A 193 N VAL A 185 SHEET 3 F 5 GLU A 206 ASP A 213 -1 O ALA A 208 N VAL A 200 SHEET 4 F 5 THR A 227 PHE A 231 -1 O LEU A 229 N TRP A 207 SHEET 5 F 5 LEU A 237 SER A 239 -1 O GLU A 238 N LYS A 230 SHEET 1 G 2 ALA A 326 SER A 327 0 SHEET 2 G 2 TRP A 333 ALA A 334 -1 O ALA A 334 N ALA A 326 CISPEP 1 THR A 123 PRO A 124 0 3.44 CISPEP 2 THR A 167 PRO A 168 0 -8.23 CISPEP 3 PRO A 285 GLY A 286 0 -0.02 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 0.002976 0.000000 0.000000 0.00000 SCALE2 0.000000 0.002976 0.000000 0.00000 SCALE3 0.000000 0.000000 0.002976 0.00000