[English] 日本語
Yorodumi
- PDB-5zj0: Crystal structure of Xanthomonas campestris FlgL (space group C2) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zj0
TitleCrystal structure of Xanthomonas campestris FlgL (space group C2)
ComponentsFlagellar hook protein FlgL
KeywordsSTRUCTURAL PROTEIN / flagellum / junction
Function / homology
Function and homology information


bacterial-type flagellum hook / bacterial-type flagellum-dependent cell motility / structural molecule activity / extracellular region
Similarity search - Function
Flagellar hook-associated protein 3 / Flagellin / Flagellin, N-terminal domain / Bacterial flagellin N-terminal helical region
Similarity search - Domain/homology
Flagellar hook protein FlgL / Flagellar hook protein FlgL
Similarity search - Component
Biological speciesXanthomonas campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHong, H.J. / Kim, T.H. / Song, W.S. / Yoon, S.I.
CitationJournal: Sci Rep / Year: 2018
Title: Crystal structure of FlgL and its implications for flagellar assembly
Authors: Hong, H.J. / Kim, T.H. / Song, W.S. / Ko, H.J. / Lee, G.S. / Kang, S.G. / Kim, P.H. / Yoon, S.I.
History
DepositionMar 18, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Flagellar hook protein FlgL


Theoretical massNumber of molelcules
Total (without water)34,0171
Polymers34,0171
Non-polymers00
Water2,684149
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14890 Å2
2
A: Flagellar hook protein FlgL

A: Flagellar hook protein FlgL


Theoretical massNumber of molelcules
Total (without water)68,0342
Polymers68,0342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y,-z-11
Buried area1650 Å2
ΔGint-22 kcal/mol
Surface area28130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.182, 63.695, 51.284
Angle α, β, γ (deg.)90.00, 105.16, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-465-

HOH

21A-478-

HOH

-
Components

#1: Protein Flagellar hook protein FlgL


Mass: 34016.879 Da / Num. of mol.: 1 / Fragment: UNP residues 4-364 / Mutation: A340V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris (bacteria) / Gene: RT95_19740 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: A0A0D0KCW5, UniProt: A0A3E1L4S6*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 19% PEG6000, 0.1M Hepes, pH 7.0, and 1.0M lithium chloride

-
Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1.00004 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 24596 / % possible obs: 98.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 25
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 1209

-
Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZIZ

5ziz


Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.921 / SU B: 8.096 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.157 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2512 1164 4.8 %RANDOM
Rwork0.20662 ---
obs0.20871 23167 98.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 31.038 Å2
Baniso -1Baniso -2Baniso -3
1--1.15 Å20 Å20.13 Å2
2--1.19 Å20 Å2
3---0.04 Å2
Refinement stepCycle: 1 / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2248 0 0 149 2397
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0212280
X-RAY DIFFRACTIONr_bond_other_d0.0010.021452
X-RAY DIFFRACTIONr_angle_refined_deg1.2111.9493095
X-RAY DIFFRACTIONr_angle_other_deg0.88633570
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5925311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.16525.8100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.64615370
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0781513
X-RAY DIFFRACTIONr_chiral_restr0.0690.2368
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022644
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02428
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5721.51530
X-RAY DIFFRACTIONr_mcbond_other0.1441.5639
X-RAY DIFFRACTIONr_mcangle_it1.06122438
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1673750
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2494.5655
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 81 -
Rwork0.306 1644 -
obs--97.29 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.31210.12112.24270.52730.15132.0309-0.13010.25880.32860.0033-0.06630.0728-0.2583-0.01650.19640.16040.0351-0.05380.34070.01880.0647-12.11-10.5743.863
22.9938-0.07963.09820.5181-0.93825.33010.08110.0838-0.1036-0.02960.0440.08320.2607-0.413-0.12510.1610.0109-0.03960.4604-0.05520.0724-21.524-19.5663.145
34.5209-2.1033-0.68412.50360.45992.45690.06820.1793-0.66170.0096-0.1810.26510.46630.36060.11280.25960.1074-0.0480.35410.01970.116412.22-34.88912.152
42.60580.01571.70140.4439-0.14311.7351-0.0030.49950.2119-0.0248-0.13070.07440.12490.36370.13370.12530.0237-0.04240.36570.0140.0512-10.118-15.710.677
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A54 - 128
2X-RAY DIFFRACTION2A129 - 188
3X-RAY DIFFRACTION3A189 - 282
4X-RAY DIFFRACTION4A283 - 362

+
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