[English] 日本語
Yorodumi
- PDB-5ziz: Crystal structure of Xanthomonas campestris FlgL (space group H3) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ziz
TitleCrystal structure of Xanthomonas campestris FlgL (space group H3)
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 / SAD / Resolution: 2.2 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 1.1Mar 27, 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 hook protein FlgL
B: Flagellar hook protein FlgL


Theoretical massNumber of molelcules
Total (without water)67,2832
Polymers67,2832
Non-polymers00
Water2,342130
1
A: Flagellar hook protein FlgL


Theoretical massNumber of molelcules
Total (without water)33,6421
Polymers33,6421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Flagellar hook protein FlgL


Theoretical massNumber of molelcules
Total (without water)33,6421
Polymers33,6421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-14 kcal/mol
Surface area25590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.372, 179.372, 54.755
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14A
24B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A48 - 128
2115B48 - 128
1125A129 - 138
2125B129 - 138
1225A146 - 188
2225B146 - 188
1135A189 - 235
2135B189 - 235
1235A248 - 282
2235B248 - 282
1145A283 - 347
2145B283 - 347

NCS ensembles :
ID
1
2
3
4

-
Components

#1: Protein Flagellar hook protein FlgL


Mass: 33641.719 Da / Num. of mol.: 2 / Fragment: UNP residues 48-364 / Mutation: A340V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris (bacteria) / Gene: RT95_19740 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0D0KCW5, UniProt: A0A3E1L4S6*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 17% PEG 3350, 0.3M magnesium nitrate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1.00004 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 33440 / % possible obs: 99.9 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 21.9
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 0.516 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 1673

-
Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.912 / SU B: 12.709 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.268 / ESU R Free: 0.218 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25795 1600 4.8 %RANDOM
Rwork0.20846 ---
obs0.21082 31707 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 39.305 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20.14 Å20 Å2
2--0.29 Å20 Å2
3----0.43 Å2
Refinement stepCycle: 1 / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4374 0 0 130 4504
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0214415
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2681.9475986
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7055600
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.33125.579190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.93115700
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4231526
X-RAY DIFFRACTIONr_chiral_restr0.0770.2714
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023344
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.5671.52981
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.08824729
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.02631434
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.354.51257
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
Refine LS restraints NCS

Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDNumberTypeRms dev position (Å)Weight position
11292medium positional0.070.5
22212medium positional0.090.5
33308medium positional0.120.5
44260medium positional0.080.5
11240loose positional0.225
22196loose positional0.185
33234loose positional0.195
44206loose positional0.145
11292medium thermal0.442
22212medium thermal0.662
33308medium thermal0.492
44260medium thermal0.42
11240loose thermal0.6710
22196loose thermal0.7310
33234loose thermal0.8110
44206loose thermal0.6110
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 120 -
Rwork0.275 2363 -
obs--100 %
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)
20.9041-1.2453-1.18384.33291.60823.2090.0527-0.0215-0.09510.0743-0.0309-0.10090.3346-0.0322-0.02180.2868-0.0061-0.02870.2804-0.03990.0791-27.336-15.46227.755
33.91580.8738-0.44443.0815-0.06120.9694-0.0915-0.1068-0.0458-0.08590.0255-0.3783-0.13540.17260.0660.31040.00710.01030.27310.00520.064-17.49121.0930.985
40.51110.1097-0.02612.94331.15061.0291-0.02820.0255-0.074-0.2431-0.02890.0123-0.0247-0.21040.05710.3103-0.02350.00650.2373-0.02540.021-31.943-2.20723.969
50.87-0.1117-0.08097.05012.82382.3135-0.0650.0305-0.02380.0089-0.09810.38040.0604-0.31030.16310.24250.01790.02230.3329-0.00430.0488-40.11811.3929.348
60.31030.1399-0.1233.58933.31723.8119-0.01820.09070.1088-0.44420.0334-0.1342-0.4904-0.046-0.01520.4170.0304-0.00250.3124-0.01410.1321-31.35822.3538.39
72.60480.3869-0.379111.5220.11191.34410.04950.0062-0.0540.0997-0.3411-2.05140.46440.2980.29150.48210.09640.04660.33370.11190.4506-14.456-11.2715.093
80.6194-0.4086-0.26572.3611.24592.1685-0.0743-0.00130.07730.0748-0.03050.04180.0547-0.14120.10480.2760.02520.00930.2606-0.01150.035-32.8929.42313.367
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION2A129 - 188
2X-RAY DIFFRACTION3A189 - 282
3X-RAY DIFFRACTION4A283 - 363
4X-RAY DIFFRACTION5B56 - 128
5X-RAY DIFFRACTION6B129 - 188
6X-RAY DIFFRACTION7B189 - 282
7X-RAY DIFFRACTION8B283 - 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