[English] 日本語
Yorodumi
- PDB-4czh: C. crescentus MreB, single filament, ADP, MP265 inhibitor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4czh
TitleC. crescentus MreB, single filament, ADP, MP265 inhibitor
ComponentsROD SHAPE-DETERMINING PROTEIN MREB
KeywordsSTRUCTURAL PROTEIN / BACTERIAL ACTIN / BACTERIAL CYTOSKELETON
Function / homology
Function and homology information


cell morphogenesis / regulation of cell shape / ATP binding / cytoplasm
Similarity search - Function
Cell shape determining protein MreB / : / MreB/Mbl protein / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / 4-chlorobenzyl carbamimidothioate / Cell shape-determining protein MreB / Cell shape-determining protein MreB
Similarity search - Component
Biological speciesCAULOBACTER VIBRIOIDES (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.644 Å
AuthorsLowe, J. / vandenEnt, F.
CitationJournal: Elife / Year: 2014
Title: Bacterial Actin Mreb Forms Antiparallel Double Filaments.
Authors: Van Den Ent, F. / Izore, T. / Bharat, T.A. / Johnson, C.M. / Lowe, J.
History
DepositionApr 19, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2014Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Other
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ROD SHAPE-DETERMINING PROTEIN MREB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5184
Polymers36,8651
Non-polymers6523
Water6,161342
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.618, 73.739, 53.700
Angle α, β, γ (deg.)90.00, 102.38, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein ROD SHAPE-DETERMINING PROTEIN MREB


Mass: 36865.496 Da / Num. of mol.: 1 / Fragment: RESIDUES 9-347 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: M-I9-CCMREB(F102S, V103G)-A347-GSHHHHHH / Source: (gene. exp.) CAULOBACTER VIBRIOIDES (bacteria) / Plasmid: PHIS17 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: B8H609, UniProt: A0A0H3C7V4*PLUS
#2: Chemical ChemComp-F90 / 4-chlorobenzyl carbamimidothioate


Mass: 200.688 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H9ClN2S
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsS-(4-CHLOROBENZYL)ISOTHIOURONIUM CHLORIDE (F90): ALFA AESAR B25362

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.68 % / Description: NONE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418
DetectorType: MARESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. obs: 45534 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 23.9 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14
Reflection shellResolution: 1.64→1.73 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.2 / % possible all: 95

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JCE

1jce


Resolution: 1.644→26.226 Å / SU ML: 0.43 / σ(F): 1.42 / Phase error: 26.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2323 4528 5 %
Rwork0.2005 --
obs0.2021 46164 97.53 %
Solvent computationShrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.822 Å2 / ksol: 0.468 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.6936 Å20 Å21.4017 Å2
2--1.0267 Å20 Å2
3---8.6668 Å2
Refinement stepCycle: LAST / Resolution: 1.644→26.226 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2370 0 40 342 2752
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162438
X-RAY DIFFRACTIONf_angle_d1.673298
X-RAY DIFFRACTIONf_dihedral_angle_d14.193924
X-RAY DIFFRACTIONf_chiral_restr0.102389
X-RAY DIFFRACTIONf_plane_restr0.009428
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6441-1.66280.37411440.34212139X-RAY DIFFRACTION74
1.6628-1.68240.3721670.31842909X-RAY DIFFRACTION98
1.6824-1.70290.37531460.29352838X-RAY DIFFRACTION100
1.7029-1.72440.31831240.27733017X-RAY DIFFRACTION100
1.7244-1.74710.2671670.2632871X-RAY DIFFRACTION100
1.7471-1.7710.35771860.25582844X-RAY DIFFRACTION100
1.771-1.79630.24761850.24862938X-RAY DIFFRACTION100
1.7963-1.82310.31091630.24312900X-RAY DIFFRACTION100
1.8231-1.85160.21631470.23482901X-RAY DIFFRACTION100
1.8516-1.8820.24591350.24342892X-RAY DIFFRACTION99
1.882-1.91440.33061480.23772916X-RAY DIFFRACTION100
1.9144-1.94920.28311490.21722937X-RAY DIFFRACTION99
1.9492-1.98670.2261460.22452965X-RAY DIFFRACTION99
1.9867-2.02720.26961390.20892877X-RAY DIFFRACTION99
2.0272-2.07130.2631660.21882859X-RAY DIFFRACTION100
2.0713-2.11950.24881380.21372941X-RAY DIFFRACTION99
2.1195-2.17240.25431340.21522897X-RAY DIFFRACTION99
2.1724-2.23110.2411580.20482881X-RAY DIFFRACTION99
2.2311-2.29680.20811310.20762917X-RAY DIFFRACTION99
2.2968-2.37080.28871540.20292832X-RAY DIFFRACTION98
2.3708-2.45550.22231420.20572919X-RAY DIFFRACTION98
2.4555-2.55380.24861550.20642874X-RAY DIFFRACTION98
2.5538-2.66990.24171650.19852844X-RAY DIFFRACTION98
2.6699-2.81050.21871400.19122870X-RAY DIFFRACTION98
2.8105-2.98630.23081460.18682856X-RAY DIFFRACTION98
2.9863-3.21650.21881480.18412818X-RAY DIFFRACTION97
3.2165-3.53950.19471600.17832843X-RAY DIFFRACTION98
3.5395-4.05010.20111630.17282880X-RAY DIFFRACTION98
4.0501-5.09660.16241280.16382819X-RAY DIFFRACTION97
5.0966-26.2290.22861540.20542440X-RAY DIFFRACTION84

+
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