PDB Short entry for 2BGZ HEADER MOTOR PROTEIN 06-JAN-05 2BGZ TITLE ATOMIC MODEL OF THE BACTERIAL FLAGELLAR BASED ON DOCKING AN X-RAY TITLE 2 DERIVED HOOK STRUCTURE INTO AN EM MAP. COMPND MOL_ID: 1; COMPND 2 MOLECULE: FLAGELLAR HOOK PROTEIN FLGE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: FLGE31, RESIDUES 71-369; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: FIT OF CRYSTAL STRUCTURE PDB ID 1WLG TO AN EM AMAP OF COMPND 7 S. TYPHIMURIUM POLYHOOK SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SALMONELLA TYPHIMURIUM; SOURCE 3 ORGANISM_TAXID: 602; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MOTOR PROTEIN, BACTERIAL MOTIILITY, BACTERIAL FLAGELLAR HOOK, KEYWDS 2 FLAGELLUM EXPDTA ELECTRON MICROSCOPY AUTHOR T.R.SHAIKH,D.R.THOMAS,J.Z.CHEN,F.A.SAMATEY,H.MATSUNAMI,K.IMADA, AUTHOR 2 K.NAMBA,D.J.DEROSIER REVDAT 7 23-AUG-17 2BGZ 1 REMARK REVDAT 6 21-APR-10 2BGZ 1 VERSN REVDAT 5 24-FEB-09 2BGZ 1 VERSN REVDAT 4 22-JUL-08 2BGZ 1 REMARK REVDAT 3 11-SEP-07 2BGZ 1 REMARK REVDAT 2 09-FEB-06 2BGZ 1 REMARK REVDAT 1 27-JAN-05 2BGZ 0 JRNL AUTH T.R.SHAIKH,D.R.THOMAS,J.Z.CHEN,F.A.SAMATEY,H.MATSUNAMI, JRNL AUTH 2 K.IMADA,K.NAMBA,D.J.DEROSIER JRNL TITL A PARTIAL ATOMIC STRUCTURE FOR THE FLAGELLAR HOOK OF JRNL TITL 2 SALMONELLA TYPHIMURIUM. JRNL REF PROC.NATL.ACAD.SCI.USA V. 102 1023 2005 JRNL REFN ISSN 0027-8424 JRNL PMID 15657146 JRNL DOI 10.1073/PNAS.0409020102 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH F.A.SAMATEY,H.MATSUNAMI,K.IMADA,S.NAGASHIMA,T.R.SHAIKH, REMARK 1 AUTH 2 D.R.THOMAS,J.Z.CHEN,D.J.DEROSIER,A.KITAO,K.NAMBA REMARK 1 TITL STRUCTURE OF THE BACTERIAL FLAGELLAR HOOK AND IMPLICATION REMARK 1 TITL 2 FOR THE MOLECULAR UNIVERSAL JOINT MECHANISM. REMARK 1 REF NATURE V. 431 1062 2004 REMARK 1 REFN ISSN 0028-0836 REMARK 1 PMID 15510139 REMARK 1 DOI 10.1038/NATURE02997 REMARK 2 REMARK 2 RESOLUTION. 12.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RSREF, BRANDEIS HELICAL PACKAGE 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 : OTHER REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : METHOD--RECIPROCAL SPACE FITTING IN URO 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) : 9.000 REMARK 3 NUMBER OF PARTICLES : NULL REMARK 3 CTF CORRECTION METHOD : NULL REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: HELICAL SYMMETRY OPERATORS CAN BE CALCULATED USING REMARK 3 RISE PER SUBUNIT 4.226475A ROTATION PER SUBUNIT 23.48758 DEG. REMARK 3 DATA USED IN REFINEMENT. RESOLUTION RANGE HIGH 12A, RESOLUTION REMARK 3 RANGE LOW 200A, DATA CUTOFF (SIGMA(F)) 1, COMPLETENESS FOR RANGE REMARK 3 100(%) NUMBER OF REFLECTIONS 84. PROTEIN ATOMS 2156 REMARK 4 REMARK 4 2BGZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE. REMARK 100 THE DEPOSITION ID IS D_1290022132. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : CRYSTALLOGRAPHY REMARK 245 SPECIMEN TYPE : VITREOUS ICE (CRYO EM) REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : 2D ARRAY REMARK 245 PARTICLE TYPE : HELICAL REMARK 245 NAME OF SAMPLE : POLYHOOK REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : HOLEY CARBON REMARK 245 SAMPLE VITRIFICATION DETAILS : SAMPLES PREPARED AT 4 DEG C REMARK 245 PLUNGED INTO LIQUID ETHANE REMARK 245 SAMPLE BUFFER : 10 MM TRIS/HCL,5MM EDTA,0. REMARK 245 1%V/V TRITON X-100 REMARK 245 PH : 8.00 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI/PHILIPS CM200FEG REMARK 245 DETECTOR TYPE : KODAK SO-163 FILM REMARK 245 MINIMUM DEFOCUS (NM) : 1300.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2700.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.00 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 10.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 66000 REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 200 REMARK 245 IMAGING DETAILS : DATA FROM 262 INDIVIDUAL REMARK 245 SEGMENTS OF HOOK IN FINAL MAP. 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 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 ASN A 364 REMARK 465 VAL A 365 REMARK 465 ASP A 366 REMARK 465 LEU A 367 REMARK 465 SER A 368 REMARK 465 LYS A 369 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 CA PRO A 139 N ASN A 140 1.19 REMARK 500 C PRO A 139 CA ASN A 140 1.36 REMARK 500 CD1 LEU A 288 CA TYR A 303 1.73 REMARK 500 CG LEU A 288 N VAL A 289 1.77 REMARK 500 CD2 LEU A 288 O ASN A 302 1.81 REMARK 500 CD1 LEU A 288 C TYR A 303 1.84 REMARK 500 CD1 LEU A 288 N SER A 304 1.98 REMARK 500 CD ARG A 105 ND2 ASN A 140 2.17 REMARK 500 REMARK 500 REMARK: NULL 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. = 4.2 DEGREES REMARK 500 ARG A 105 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 PRO A 139 CA - C - N ANGL. DEV. = -67.1 DEGREES REMARK 500 PRO A 139 O - C - N ANGL. DEV. = 34.9 DEGREES REMARK 500 ASN A 140 C - N - CA ANGL. DEV. = -61.3 DEGREES REMARK 500 MET A 143 CG - SD - CE ANGL. DEV. = 9.6 DEGREES REMARK 500 LEU A 288 CB - CA - C ANGL. DEV. = -13.7 DEGREES REMARK 500 VAL A 289 N - CA - C ANGL. DEV. = 17.4 DEGREES REMARK 500 ASP A 330 CB - CG - OD2 ANGL. DEV. = 5.4 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 LEU A 263 131.60 -39.62 REMARK 500 ASN A 264 -0.39 80.00 REMARK 500 PRO A 285 107.94 -54.02 REMARK 500 LEU A 288 -120.93 -114.10 REMARK 500 VAL A 289 -76.72 -148.16 REMARK 500 ASP A 330 -145.09 50.11 REMARK 500 ASN A 357 -55.41 -151.70 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 PRO A 139 -10.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1WLG RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF FLGE31, A MAJOR FRAGMENT OF THE HOOKPROTEIN REMARK 900 RELATED ID: 2BGY RELATED DB: PDB REMARK 900 FIT OF THE X-RAY STRUCTURE OF THE BACTERIAL FLAGELLAR HOOK FRAGMENT REMARK 900 FLGE31 INTO AN EM MAP FROM THE HOOK OF CAULOBACTER CRESCENTUS. REMARK 900 RELATED ID: EMD-1132 RELATED DB: EMDB REMARK 900 A PARTIAL ATOMIC STRUCTURE FOR THE FLAGELLAR HOOK OF SALMONELLA REMARK 900 TYPHIMURIUM DBREF 2BGZ A 71 369 UNP P16322 FLGE_SALTY 71 369 SEQRES 1 A 299 GLY LEU ASP VAL ALA ILE SER GLN ASN GLY PHE PHE ARG SEQRES 2 A 299 LEU VAL ASP SER ASN GLY SER VAL PHE TYR SER ARG ASN SEQRES 3 A 299 GLY GLN PHE LYS LEU ASP GLU ASN ARG ASN LEU VAL ASN SEQRES 4 A 299 MET GLN GLY MET GLN LEU THR GLY TYR PRO ALA THR GLY SEQRES 5 A 299 THR PRO PRO THR ILE GLN GLN GLY ALA ASN PRO ALA PRO SEQRES 6 A 299 ILE THR ILE PRO ASN THR LEU MET ALA ALA LYS SER THR SEQRES 7 A 299 THR THR ALA SER MET GLN ILE ASN LEU ASN SER THR ASP SEQRES 8 A 299 PRO VAL PRO SER LYS THR PRO PHE SER VAL SER ASP ALA SEQRES 9 A 299 ASP SER TYR ASN LYS LYS GLY THR VAL THR VAL TYR ASP SEQRES 10 A 299 SER GLN GLY ASN ALA HIS ASP MET ASN VAL TYR PHE VAL SEQRES 11 A 299 LYS THR LYS ASP ASN GLU TRP ALA VAL TYR THR HIS ASP SEQRES 12 A 299 SER SER ASP PRO ALA ALA THR ALA PRO THR THR ALA SER SEQRES 13 A 299 THR THR LEU LYS PHE ASN GLU ASN GLY ILE LEU GLU SER SEQRES 14 A 299 GLY GLY THR VAL ASN ILE THR THR GLY THR ILE ASN GLY SEQRES 15 A 299 ALA THR ALA ALA THR PHE SER LEU SER PHE LEU ASN SER SEQRES 16 A 299 MET GLN GLN ASN THR GLY ALA ASN ASN ILE VAL ALA THR SEQRES 17 A 299 ASN GLN ASN GLY TYR LYS PRO GLY ASP LEU VAL SER TYR SEQRES 18 A 299 GLN ILE ASN ASN ASP GLY THR VAL VAL GLY ASN TYR SER SEQRES 19 A 299 ASN GLU GLN GLU GLN VAL LEU GLY GLN ILE VAL LEU ALA SEQRES 20 A 299 ASN PHE ALA ASN ASN GLU GLY LEU ALA SER GLN GLY ASP SEQRES 21 A 299 ASN VAL TRP ALA ALA THR GLN ALA SER GLY VAL ALA LEU SEQRES 22 A 299 LEU GLY THR ALA GLY SER GLY ASN PHE GLY LYS LEU THR SEQRES 23 A 299 ASN GLY ALA LEU GLU ALA SER ASN VAL ASP LEU SER LYS HELIX 1 1 ASN A 321 LEU A 325 5 5 SHEET 1 AA 3 LEU A 72 ASP A 73 0 SHEET 2 AA 3 GLN A 98 LEU A 101 -1 O PHE A 99 N LEU A 72 SHEET 3 AA 3 LEU A 107 VAL A 108 -1 O VAL A 108 N LYS A 100 SHEET 1 AB 3 ALA A 134 PRO A 135 0 SHEET 2 AB 3 GLN A 114 TYR A 118 -1 O GLY A 117 N ALA A 134 SHEET 3 AB 3 PHE A 81 VAL A 85 -1 O ARG A 83 N THR A 116 SHEET 1 AC 6 ALA A 134 PRO A 135 0 SHEET 2 AC 6 GLN A 114 TYR A 118 -1 O GLY A 117 N ALA A 134 SHEET 3 AC 6 GLU A 308 ILE A 314 -1 O GLN A 313 N TYR A 118 SHEET 4 AC 6 THR A 298 ASN A 302 -1 O VAL A 299 N LEU A 311 SHEET 5 AC 6 SER A 290 ILE A 293 -1 O SER A 290 N ASN A 302 SHEET 6 AC 6 ALA A 359 ALA A 362 -1 O ALA A 359 N ILE A 293 SHEET 1 AD 4 THR A 242 THR A 246 0 SHEET 2 AD 4 THR A 257 SER A 261 -1 O PHE A 258 N ILE A 245 SHEET 3 AD 4 THR A 150 ASN A 158 1 O ALA A 151 N SER A 261 SHEET 4 AD 4 ASN A 274 GLN A 280 -1 O ASN A 274 N ASN A 156 SHEET 1 AE 4 THR A 242 THR A 246 0 SHEET 2 AE 4 THR A 257 SER A 261 -1 O PHE A 258 N ILE A 245 SHEET 3 AE 4 THR A 150 ASN A 158 1 O ALA A 151 N SER A 261 SHEET 4 AE 4 MET A 266 GLN A 268 1 O MET A 266 N LEU A 157 SHEET 1 AF 5 LYS A 179 TYR A 186 0 SHEET 2 AF 5 ALA A 192 LYS A 203 -1 O HIS A 193 N VAL A 185 SHEET 3 AF 5 GLU A 206 ASP A 213 -1 O GLU A 206 N THR A 202 SHEET 4 AF 5 THR A 227 PHE A 231 -1 O THR A 227 N VAL A 209 SHEET 5 AF 5 LEU A 237 SER A 239 -1 N GLU A 238 O LYS A 230 CISPEP 1 THR A 123 PRO A 124 0 3.72 CISPEP 2 THR A 167 PRO A 168 0 -7.95 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000