[English] 日本語
Yorodumi
- PDB-7lkm: The PilB(N-terminal_P70S mutant)-PilZ complex of the Type IV pilu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7lkm
TitleThe PilB(N-terminal_P70S mutant)-PilZ complex of the Type IV pilus from Xanthomonas citri
Components
  • Pilus biogenesis protein
  • Type IV fimbriae assembly protein
KeywordsTRANSPORT PROTEIN / Type IV pilus
Function / homology
Function and homology information


pilus assembly / cyclic-di-GMP binding / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
ATPase, type IV, pilus assembly, PilB / Type II secretion system protein GspE, N-terminal / MshEN domain / Type II secretion system protein GspE, N-terminal superfamily / PilZ domain / PilZ domain / Bacterial type II secretion system protein E signature. / Type II/IV secretion system protein / Type II/IV secretion system protein / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Pilus biogenesis protein / Type IV fimbriae assembly protein
Similarity search - Component
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLlontop, E.E. / Guzzo, C.R. / Farah, C.S.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2017/17303-7 Brazil
CitationJournal: Plos Pathog. / Year: 2021
Title: The PilB-PilZ-FimX regulatory complex of the Type IV pilus from Xanthomonas citri.
Authors: Llontop, E.E. / Cenens, W. / Favaro, D.C. / Sgro, G.G. / Salinas, R.K. / Guzzo, C.R. / Farah, C.S.
History
DepositionFeb 2, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 1, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pilus biogenesis protein
B: Pilus biogenesis protein
C: Type IV fimbriae assembly protein
D: Type IV fimbriae assembly protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0249
Polymers62,5434
Non-polymers4805
Water7,981443
1
A: Pilus biogenesis protein
C: Type IV fimbriae assembly protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5605
Polymers31,2722
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pilus biogenesis protein
D: Type IV fimbriae assembly protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4644
Polymers31,2722
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.063, 122.408, 62.730
Angle α, β, γ (deg.)90.000, 98.980, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 10 or resid 12 through 46...
d_2ens_1(chain "B" and ((resid 10 and (name N or name...
d_1ens_2(chain "C" and (resid 10 through 15 or (resid 16...
d_2ens_2(chain "D" and (resid 10 through 17 or resid 19...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1HISHISA2
d_12ens_1ILEGLNA5 - 39
d_13ens_1PHEHISA41 - 88
d_14ens_1VALASNA90 - 98
d_15ens_1LEUILEA101 - 117
d_16ens_1HISTHRA122 - 123
d_17ens_1LEUSERA125 - 153
d_21ens_1HISHISB1
d_22ens_1ILEGLNB4 - 38
d_23ens_1PHEHISB41 - 88
d_24ens_1VALASNB91 - 99
d_25ens_1LEUILEB101 - 117
d_26ens_1HISTHRB120 - 121
d_27ens_1LEUSERB124 - 152
d_11ens_2ILEASPC3 - 10
d_12ens_2PROMETC13 - 111
d_21ens_2ILEASPD2 - 9
d_22ens_2PROMETD11 - 109

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.999413651728, -0.0176144565573, 0.0293612612036), (-0.0187105784826, -0.437203362327, -0.899168023354), (0.0286751982054, -0.89919016392, 0.436617432219)-52.3140021881, 57.1164020978, 38.3743069698
2given(-0.999706384388, 0.0240472590979, -0.00297898380836), (-0.00710793277323, -0.408561079593, -0.91270330422), (-0.0231651096769, -0.912414145863, 0.408612045982)-51.3548097329, 58.0941593085, 37.0166822777

-
Components

#1: Protein Pilus biogenesis protein


Mass: 18828.232 Da / Num. of mol.: 2 / Fragment: Residues 12-163 / Mutation: P70S
Source method: isolated from a genetically manipulated source
Details: Expressed with an N-terminal His tag
Source: (gene. exp.) Xanthomonas axonopodis pv. citri (bacteria)
Strain: 306 / Gene: pilB, XAC3239 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8PHL2
#2: Protein Type IV fimbriae assembly protein


Mass: 12443.409 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas axonopodis pv. citri (bacteria)
Strain: 306 / Gene: pilZ, XAC1133 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8PND9
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 443 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris pH 8.5; 2.0 M ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45866 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45866 Å / Relative weight: 1
ReflectionResolution: 2→28 Å / Num. obs: 44979 / % possible obs: 99.6 % / Redundancy: 5 % / Biso Wilson estimate: 23.42 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 10.1
Reflection shellResolution: 2→3.1 Å / Rmerge(I) obs: 1.25 / Num. unique obs: 4457

-
Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PilB-PilZ_SeMet_Model

Resolution: 2→28 Å / SU ML: 0.2587 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 22.8292
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2274 1935 4.94 %
Rwork0.1791 37220 -
obs0.1815 39155 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.23 Å2
Refinement stepCycle: LAST / Resolution: 2→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3863 0 25 443 4331
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01044052
X-RAY DIFFRACTIONf_angle_d1.50035524
X-RAY DIFFRACTIONf_chiral_restr0.071642
X-RAY DIFFRACTIONf_plane_restr0.0113718
X-RAY DIFFRACTIONf_dihedral_angle_d21.6593560
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.30658820501
ens_2d_2CX-RAY DIFFRACTIONTorsion NCS0.788191403179
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.32731410.262692X-RAY DIFFRACTION99.58
2.05-2.110.30291370.23722608X-RAY DIFFRACTION99.75
2.11-2.170.30041370.22362675X-RAY DIFFRACTION99.68
2.17-2.240.26651130.21122649X-RAY DIFFRACTION99.28
2.24-2.320.24961340.20072672X-RAY DIFFRACTION99.57
2.32-2.410.26361060.19042653X-RAY DIFFRACTION99.57
2.41-2.520.24711470.19062645X-RAY DIFFRACTION99.64
2.52-2.650.25011240.19012654X-RAY DIFFRACTION99.46
2.65-2.820.23491350.19312672X-RAY DIFFRACTION99.61
2.82-3.040.24231490.17952643X-RAY DIFFRACTION99.86
3.04-3.340.21931530.17622652X-RAY DIFFRACTION99.86
3.34-3.820.21841640.15162652X-RAY DIFFRACTION99.93
3.82-4.810.17431420.13972668X-RAY DIFFRACTION99.96
4.81-28.030.18811530.16752685X-RAY DIFFRACTION99.58

+
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://pdbjlvh1.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