[English] 日本語
Yorodumi
- PDB-3c12: Crystal Structure of FlgD from Xanthomonas campestris: Insights i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3c12
TitleCrystal Structure of FlgD from Xanthomonas campestris: Insights into the Hook Capping Essential for Flagellar Assembly
ComponentsFlagellar proteinFlagellum
KeywordsBIOSYNTHETIC PROTEIN / FlgD / hook capping / Xanthomonas campestris / Ig-like domain / Fn-III domain / tudor-like domain / flagellar biogenesis / Flagellum
Function / homology
Function and homology information


bacterial-type flagellum hook / bacterial-type flagellum organization / bacterial-type flagellum-dependent swarming motility
Similarity search - Function
SH3 type barrels. - #910 / Immunoglobulin-like - #4070 / FlgD Tudor-like domain / FlgD Tudor-like domain / Flagellar hook capping protein / Flagellar hook capping protein - N-terminal region / FlgD Ig-like domain / FlgD Ig-like domain / SH3 type barrels. / Roll ...SH3 type barrels. - #910 / Immunoglobulin-like - #4070 / FlgD Tudor-like domain / FlgD Tudor-like domain / Flagellar hook capping protein / Flagellar hook capping protein - N-terminal region / FlgD Ig-like domain / FlgD Ig-like domain / SH3 type barrels. / Roll / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Basal-body rod modification protein FlgD
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.51 Å
AuthorsKuo, W.-T. / Chin, K.-H. / Lo, W.-T. / Chou, S.-H.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Crystal structure of the C-terminal domain of a flagellar hook-capping protein from Xanthomonas campestris
Authors: Kuo, W.-T. / Chin, K.-H. / Lo, W.-T. / Wang, A.H.-J. / Chou, S.-H.
History
DepositionJan 22, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Flagellar protein


Theoretical massNumber of molelcules
Total (without water)13,7381
Polymers13,7381
Non-polymers00
Water55831
1
A: Flagellar protein

A: Flagellar protein


Theoretical massNumber of molelcules
Total (without water)27,4762
Polymers27,4762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_556-x+y,y,-z+3/21
Unit cell
Length a, b, c (Å)116.710, 116.710, 71.820
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

-
Components

#1: Protein Flagellar protein / Flagellum / FlgD


Mass: 13738.245 Da / Num. of mol.: 1 / Fragment: UNP Residues 84-221
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: Q8P9B5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
Sample preparation

CrystalDensity Matthews: 5.138965 Å3/Da / Density % sol: 76.065216 %
Crystal growTemperature: 295 K / Method: vapor diffusion / Details: VAPOR DIFFUSION, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 0.97945 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 24, 2007
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 11527 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11 % / Biso Wilson estimate: 50 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 33
Reflection shellResolution: 2.54→2.64 Å / Redundancy: 11 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.3 / Num. unique all: 11527 / % possible all: 100

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.51→29.27 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 394950.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1846 9.3 %RANDOM
Rwork0.257 ---
obs0.257 11527 93.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.627 Å2 / ksol: 0.376483 e/Å3
Displacement parametersBiso mean: 55.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.91 Å26.47 Å20 Å2
2---1.91 Å20 Å2
3---3.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.54 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 2.51→29.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms967 0 0 31 998
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_mcangle_it2.342
X-RAY DIFFRACTIONc_scbond_it1.652
X-RAY DIFFRACTIONc_scangle_it2.572.5
LS refinement shellResolution: 2.51→2.61 Å / Total num. of bins used: 6 /
RfactorNum. reflection
Rwork0.272 0
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

+
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