[English] 日本語
Yorodumi
- PDB-1lkv: Crystal Structure of the Middle and C-terminal Domains of the Fla... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1lkv
TitleCrystal Structure of the Middle and C-terminal Domains of the Flagellar Rotor Protein FliG
ComponentsFLAGELLAR MOTOR SWITCH PROTEIN FLIGFlagellar motor switch protein
KeywordsSTRUCTURAL PROTEIN / chemotaxis / flagella / flagellar motion
Function / homology
Function and homology information


bacterial-type flagellum basal body / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / chemotaxis / protein heterodimerization activity / protein homodimerization activity / plasma membrane
Similarity search - Function
Flagellar motor switch protein FliG, alpha-alpha superhelical domain / Flagellar motor switch protein FliG / Flagellar motor switch protein FliG, alpha-helical / Flagellar motor switch protein FliG, C-terminal / Flagellar motor switch protein FliG, N-terminal domain / Flagellar motor switch protein FliG, middle domain / FliG C-terminal domain / FliG middle domain / FliG N-terminal domain / Annexin V; domain 1 ...Flagellar motor switch protein FliG, alpha-alpha superhelical domain / Flagellar motor switch protein FliG / Flagellar motor switch protein FliG, alpha-helical / Flagellar motor switch protein FliG, C-terminal / Flagellar motor switch protein FliG, N-terminal domain / Flagellar motor switch protein FliG, middle domain / FliG C-terminal domain / FliG middle domain / FliG N-terminal domain / Annexin V; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Flagellar motor switch protein FliG
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsBrown, P.N. / Hill, C.P. / Blair, D.F.
CitationJournal: EMBO J. / Year: 2002
Title: Crystal structure of the middle and C-terminal domains of the flagellar rotor protein FliG.
Authors: Brown, P.N. / Hill, C.P. / Blair, D.F.
History
DepositionApr 25, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
X: FLAGELLAR MOTOR SWITCH PROTEIN FLIG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4533
Polymers26,3731
Non-polymers802
Water905
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
X: FLAGELLAR MOTOR SWITCH PROTEIN FLIG
hetero molecules

X: FLAGELLAR MOTOR SWITCH PROTEIN FLIG
hetero molecules

X: FLAGELLAR MOTOR SWITCH PROTEIN FLIG
hetero molecules

X: FLAGELLAR MOTOR SWITCH PROTEIN FLIG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,81112
Polymers105,4904
Non-polymers3218
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation8_557x-y,-y,-z+21
crystal symmetry operation11_657-x+y+1,y,-z+21
Buried area15970 Å2
ΔGint-165 kcal/mol
Surface area42760 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)113.943, 113.943, 128.826
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

-
Components

#1: Protein FLAGELLAR MOTOR SWITCH PROTEIN FLIG / Flagellar motor switch protein


Mass: 26372.527 Da / Num. of mol.: 1 / Fragment: RESIDUES 104-335
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Plasmid: pPNB1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WY63
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 4.58 Å3/Da / Density % sol: 73.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: Isopropanol, CaCl2, sodium acetate, pluronic F-68, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMTris-HCl1droppH8.0
210 mM1dropNaCl
310 mg/mlprotein1drop
48-10 %(v/v)isopropanol1reservoir
5200-400 mM1reservoirCaCl2
6100 mMsodium acetate1reservoirpH4.4-5.0
71 %pluronic F-681reservoir

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL9-210.99981
SYNCHROTRONSSRL BL9-220.97935, 0.97906, 0.93222
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDMay 16, 2000
ADSC QUANTUM 42CCDFeb 6, 2001
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystal monochromatorSINGLE WAVELENGTHMx-ray1
2double crystal monochromatorMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.999811
20.979351
30.979061
40.932221
ReflectionResolution: 2.798→57 Å / Num. all: 12228 / Num. obs: 12228 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.8→2.9 Å / % possible all: 90.1
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 57.035 Å / Num. obs: 12745 / % possible obs: 96 % / Num. measured all: 179161 / Rmerge(I) obs: 0.084
Reflection shell
*PLUS
% possible obs: 90.1 % / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 3.6

-
Processing

Software
NameVersionClassification
shaken' bakemodel building
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
RefinementMethod to determine structure: MAD / Resolution: 2.8→57 Å / Cor.coef. Fo:Fc: 0.865 / Cor.coef. Fo:Fc free: 0.844 / SU ML: 0.296 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.394 / ESU R Free: 0.319 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28009 991 8.1 %RANDOM
Rwork0.25548 ---
all0.25748 12228 --
obs0.2574 11237 95.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.315 Å2
Baniso -1Baniso -2Baniso -3
1-1.79 Å20.89 Å20 Å2
2--1.79 Å20 Å2
3----2.68 Å2
Refinement stepCycle: LAST / Resolution: 2.8→57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1701 0 2 5 1708
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221718
X-RAY DIFFRACTIONr_angle_refined_deg1.9271.9992312
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8983212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.26915358
X-RAY DIFFRACTIONr_chiral_restr0.1390.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021248
X-RAY DIFFRACTIONr_nbd_refined0.1410.3733
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.5101
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0770.367
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.59
LS refinement shellResolution: 2.8→2.949 Å / Total num. of bins used: 10
RfactorNum. reflection
Rfree0.364 144
Rwork0.287 1474
obs-1474
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 35 Å / Rfactor all: 0.25748 / Rfactor obs: 0.2574 / Rfactor Rfree: 0.28 / Rfactor Rwork: 0.255
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.016
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.972
LS refinement shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å / Rfactor Rfree: 0.364 / Rfactor Rwork: 0.287

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more