[English] 日本語
Yorodumi
- PDB-8bvf: MoeA2 from Corynebacterium glutamicum in complex with FtsZ-CTD -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8bvf
TitleMoeA2 from Corynebacterium glutamicum in complex with FtsZ-CTD
Components
  • Cell division protein FtsZ
  • Molybdopterin molybdenumtransferase
KeywordsCELL CYCLE / Molybdopterin molybdotransferase / cell division / gephyrin-like protein / Corynebacteriales
Function / homology
Function and homology information


molybdopterin cofactor biosynthetic process / molybdopterin molybdotransferase / molybdopterin molybdotransferase activity / chloroplast fission / Mo-molybdopterin cofactor biosynthetic process / FtsZ-dependent cytokinesis / division septum assembly / cell division site / protein polymerization / GTPase activity ...molybdopterin cofactor biosynthetic process / molybdopterin molybdotransferase / molybdopterin molybdotransferase activity / chloroplast fission / Mo-molybdopterin cofactor biosynthetic process / FtsZ-dependent cytokinesis / division septum assembly / cell division site / protein polymerization / GTPase activity / GTP binding / metal ion binding / cytoplasm
Similarity search - Function
MoeA, N-terminal and linker domain / MoeA, C-terminal, domain IV / MoeA, N-terminal and linker domain superfamily / MoeA, C-terminal, domain IV superfamily / Molybdopterin biosynthesis protein MoeA-like / MoeA N-terminal region (domain I and II) / MoeA C-terminal region (domain IV) / MoaB/Mog domain / MoaB/Mog-like domain superfamily / Probable molybdopterin binding domain ...MoeA, N-terminal and linker domain / MoeA, C-terminal, domain IV / MoeA, N-terminal and linker domain superfamily / MoeA, C-terminal, domain IV superfamily / Molybdopterin biosynthesis protein MoeA-like / MoeA N-terminal region (domain I and II) / MoeA C-terminal region (domain IV) / MoaB/Mog domain / MoaB/Mog-like domain superfamily / Probable molybdopterin binding domain / Probable molybdopterin binding domain / Tubulin-like protein FtsZ/CetZ / Cell division protein FtsZ / Cell division protein FtsZ, conserved site / Cell division protein FtsZ, C-terminal / FtsZ family, C-terminal domain / FtsZ protein signature 1. / FtsZ protein signature 2. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily
Similarity search - Domain/homology
Cell division protein FtsZ / Molybdopterin molybdenumtransferase
Similarity search - Component
Biological speciesCorynebacterium glutamicum ATCC 13032 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsMartinez, M. / Haouz, A. / Wehenkel, A.M. / Alzari, P.M.
Funding support France, Uruguay, 3items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-18-CE11-0017 France
Agence Nationale de la Recherche (ANR)ANR-21-CE11-0003 France
Agencia Nacional de Investigacion e Innovacion (ANII)FCE_1_2019_1_155569Uruguay
CitationJournal: Biorxiv / Year: 2023
Title: Eukaryotic-like gephyrin and cognate membrane receptor coordinate corynebacterial cell division and polar elongation.
Authors: Martinez, M. / Petit, J. / Leyva, A. / Sogues, A. / Megrian, D. / Rodriguez, A. / Gaday, Q. / Ben Assaya, M. / Portela, M. / Haouz, A. / Ducret, A. / Grangeasse, C. / Alzari, P.M. / Dur N, R. / Wehenkel, A.
History
DepositionDec 3, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Molybdopterin molybdenumtransferase
B: Molybdopterin molybdenumtransferase
C: Cell division protein FtsZ
D: Cell division protein FtsZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,57114
Polymers90,7564
Non-polymers81410
Water4,234235
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7710 Å2
ΔGint-158 kcal/mol
Surface area35360 Å2
Unit cell
Length a, b, c (Å)95.580, 95.580, 229.522
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Molybdopterin molybdenumtransferase


Mass: 44229.824 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria)
Gene: Cgl0883 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8NS03
#2: Protein/peptide Cell division protein FtsZ /


Mass: 1148.220 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Corynebacterium glutamicum ATCC 13032 (bacteria)
References: UniProt: P94337
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.89 Å3/Da / Density % sol: 57.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M NaCl, 0.1M Bis-Tris pH 6.5, 1.5M (NH4)2SO4

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.68→49.2 Å / Num. obs: 30746 / % possible obs: 99.6 % / Redundancy: 9.6 % / CC1/2: 1 / Rpim(I) all: 0.05 / Net I/σ(I): 14.6
Reflection shellResolution: 2.68→2.81 Å / Num. unique obs: 3905 / CC1/2: 0.8 / Rpim(I) all: 0.296

-
Processing

Software
NameVersionClassification
PHENIX1.20.1-4487-000refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.68→49.2 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2402 1521 4.96 %
Rwork0.1843 --
obs0.187 30660 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.68→49.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5896 0 42 235 6173
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086013
X-RAY DIFFRACTIONf_angle_d0.9488173
X-RAY DIFFRACTIONf_dihedral_angle_d5.592870
X-RAY DIFFRACTIONf_chiral_restr0.057969
X-RAY DIFFRACTIONf_plane_restr0.0111076
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.68-2.770.33431430.26932474X-RAY DIFFRACTION96
2.77-2.870.2891640.22152577X-RAY DIFFRACTION100
2.87-2.980.28171220.20162617X-RAY DIFFRACTION100
2.98-3.120.26381350.20922612X-RAY DIFFRACTION100
3.12-3.280.27671080.20132675X-RAY DIFFRACTION100
3.28-3.490.25891380.19182606X-RAY DIFFRACTION100
3.49-3.750.24661300.17332659X-RAY DIFFRACTION100
3.75-4.130.21621530.15962636X-RAY DIFFRACTION100
4.13-4.730.18331400.14492677X-RAY DIFFRACTION100
4.73-5.960.2241400.17862722X-RAY DIFFRACTION100
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)
10.1956-0.419-0.61392.81963.88765.91340.0053-0.01270.0502-0.1687-0.16320.194-0.3143-0.17260.21070.23110.0055-0.00730.2530.00470.3574-7.429645.070178.3479
23.1624-1.0092-0.00633.3963-0.58942.23350.01830.1939-0.132-0.275-0.0073-0.07040.3931-0.1446-0.03810.315-0.03360.03810.2025-0.02680.27022.48629.352346.5505
36.49420.48641.31621.7927-0.91984.81-0.02790.68060.78860.06490.0678-0.0651-0.62610.8526-0.02280.4208-0.09590.16140.4909-0.01590.649722.780524.811240.3157
40.0606-1.1639-0.96643.06493.08613.2264-0.0574-0.01680.05280.14150.13980.01090.15930.1241-0.07830.2392-0.0346-0.01410.2875-0.00860.363322.75551.611247.2646
54.66780.09130.46335.0040.4514.5364-0.16340.3401-0.1278-0.47930.08920.0530.29690.07350.06940.2673-0.01510.00520.22630.00650.27569.204952.006463.5323
69.30030.77841.63026.14750.18334.7970.40971.51080.033-1.5064-0.25730.0734-0.19350.2322-0.10550.7485-0.06-0.03320.68140.10520.32296.587947.874951.1847
79.4631-7.26835.95846.4728-3.77224.4703-0.4246-1.09471.5030.77350.06740.0828-0.75980.58810.31360.724-0.3242-0.16131.18190.03590.907825.245332.258552.0804
82.5223-0.110.52822.8868-0.00012.11170.0078-0.22-0.1240.2394-0.0762-0.03440.0313-0.15050.07580.23840.0192-0.00010.2006-0.01530.23396.537633.805682.7152
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 182 )
2X-RAY DIFFRACTION2chain 'A' and (resid 183 through 330 )
3X-RAY DIFFRACTION3chain 'A' and (resid 331 through 416 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 182 )
5X-RAY DIFFRACTION5chain 'B' and (resid 331 through 418 )
6X-RAY DIFFRACTION6chain 'C' and (resid 434 through 441 )
7X-RAY DIFFRACTION7chain 'D' and (resid 434 through 439 )
8X-RAY DIFFRACTION8chain 'B' and (resid 183 through 330 )

+
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