[English] 日本語
Yorodumi
- PDB-7e1c: Structure of MreB3 from Spiroplasma eriocheiris -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7e1c
TitleStructure of MreB3 from Spiroplasma eriocheiris
ComponentsCell shape-determining protein MreB
KeywordsSTRUCTURAL PROTEIN / Cytoskeleton / actin homolog
Function / homology
Function and homology information


cell morphogenesis / regulation of cell shape / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Cell shape determining protein MreB / : / MreB/Mbl protein / Heat shock hsp70 proteins family signature 1. / Heat shock protein 70, conserved site / ATPase, nucleotide binding domain
Similarity search - Domain/homology
ACETATE ION / Cell shape-determining protein MreB
Similarity search - Component
Biological speciesSpiroplasma eriocheiris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsTakahashi, D. / Miyata, M. / Imada, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP17H01544 Japan
Japan Science and TechnologyJPMJCR19S5 Japan
CitationJournal: Open Biology / Year: 2022
Title: ATP-dependent polymerization dynamics of bacterial actin proteins involved in Spiroplasma swimming.
Authors: Takahashi, D. / Fujiwara, I. / Sasajima, Y. / Narita, A. / Imada, K. / Miyata, M.
History
DepositionFeb 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: 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: Cell shape-determining protein MreB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0523
Polymers38,9521
Non-polymers992
Water5,999333
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint-10 kcal/mol
Surface area15930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.420, 68.090, 54.570
Angle α, β, γ (deg.)90.000, 91.730, 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

-
Components

#1: Protein Cell shape-determining protein MreB


Mass: 38952.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spiroplasma eriocheiris (bacteria) / Gene: mreB3, mreB, SERIO_v1c12260 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3XJK5
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 2.5 Å3/Da / Density % sol: 50.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 20% (w/v) PEG 8000, 0.1 M MES-NaOH pH 6.0, 200 mM Ca(OAc)2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 26, 2019
RadiationMonochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→54.54 Å / Num. obs: 30343 / % possible obs: 100 % / Redundancy: 5.3 % / Biso Wilson estimate: 22.84 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.045 / Net I/σ(I): 9.8
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1962 / CC1/2: 0.866 / Rpim(I) all: 0.263 / % possible all: 100

-
Processing

Software
NameVersionClassification
BSSdata collection
PHENIX1.15.2_3472refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4czl

4czl


Resolution: 1.9→54.54 Å / SU ML: 0.2152 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.9178
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2213 2001 6.6 %
Rwork0.1854 28311 -
obs0.1878 30312 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.46 Å2
Refinement stepCycle: LAST / Resolution: 1.9→54.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2511 0 5 333 2849
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00392533
X-RAY DIFFRACTIONf_angle_d0.61373447
X-RAY DIFFRACTIONf_chiral_restr0.0469408
X-RAY DIFFRACTIONf_plane_restr0.0031428
X-RAY DIFFRACTIONf_dihedral_angle_d14.2548969
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.2811270.2542032X-RAY DIFFRACTION99.86
1.95-20.2941460.23471985X-RAY DIFFRACTION100
2-2.060.24051480.22582001X-RAY DIFFRACTION99.63
2.06-2.130.29241440.21282013X-RAY DIFFRACTION99.91
2.13-2.20.24991440.20092008X-RAY DIFFRACTION99.95
2.2-2.290.23951530.19952013X-RAY DIFFRACTION100
2.29-2.390.25581430.19452013X-RAY DIFFRACTION99.95
2.39-2.520.21921360.19422018X-RAY DIFFRACTION99.86
2.52-2.680.23271450.18831999X-RAY DIFFRACTION100
2.68-2.880.20411450.19042030X-RAY DIFFRACTION100
2.88-3.170.21051330.18012042X-RAY DIFFRACTION100
3.17-3.630.20651440.16642038X-RAY DIFFRACTION100
3.63-4.580.18311420.15232047X-RAY DIFFRACTION100
4.58-54.540.20861510.18442072X-RAY DIFFRACTION99.91

+
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