[English] 日本語
Yorodumi
- PDB-5zul: Small heat shock protein from Mycobacterium marinum M : Form-3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zul
TitleSmall heat shock protein from Mycobacterium marinum M : Form-3
ComponentsSmall heat shock protein
KeywordsCHAPERONE / sHSP / oligomers / polydispersity
Function / homology: / Hsp20/alpha crystallin family / Small heat shock protein (sHSP) domain profile. / Alpha crystallin/Hsp20 domain / HSP20-like chaperone / Molecular chaperone (Small heat shock protein)
Function and homology information
Biological speciesMycobacterium marinum M (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.75 Å
AuthorsBhandari, S. / Suguna, K.
Funding support India, 1items
OrganizationGrant numberCountry
India
CitationJournal: Proteins / Year: 2019
Title: Dodecameric structure of a small heat shock protein from Mycobacterium marinum M.
Authors: Bhandari, S. / Biswas, S. / Chaudhary, A. / Dutta, S. / Suguna, K.
History
DepositionMay 8, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Small heat shock protein
B: Small heat shock protein
C: Small heat shock protein
D: Small heat shock protein
E: Small heat shock protein
F: Small heat shock protein


Theoretical massNumber of molelcules
Total (without water)99,2156
Polymers99,2156
Non-polymers00
Water0
1
A: Small heat shock protein
B: Small heat shock protein
C: Small heat shock protein
D: Small heat shock protein
E: Small heat shock protein
F: Small heat shock protein

A: Small heat shock protein
B: Small heat shock protein
C: Small heat shock protein
D: Small heat shock protein
E: Small heat shock protein
F: Small heat shock protein


Theoretical massNumber of molelcules
Total (without water)198,43012
Polymers198,43012
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_575x,-y+2,-z1
Buried area19730 Å2
ΔGint-100 kcal/mol
Surface area67960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.209, 128.420, 135.379
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein
Small heat shock protein


Mass: 16535.803 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium marinum M (bacteria) / Strain: M / Gene: MMAR_2991 / Plasmid: pRSET-A / Production host: Escherichia coli (E. coli) / References: UniProt: B2HF11

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.37 %
Crystal growTemperature: 293 K / Method: microbatch
Details: 0.05M MgCl2.6H2O, 0.1M HEPES pH 7.5 and 30% PEG MME 550

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.75→74.901 Å / Num. obs: 8296 / % possible obs: 97.1 % / Redundancy: 9.3 % / Biso Wilson estimate: 114.3 Å2 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.039 / Net I/σ(I): 8.9
Reflection shellResolution: 3.75→4.19 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.724 / Num. unique obs: 2137 / CC1/2: 0.88 / Rpim(I) all: 0.254 / % possible all: 90.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZS3

5zs3


Resolution: 3.75→74.9 Å / Cor.coef. Fo:Fc: 0.84 / Cor.coef. Fo:Fc free: 0.807 / SU B: 0.02 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.991 / ESU R Free: 1.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.40672 395 4.8 %RANDOM
Rwork0.36643 ---
obs0.36842 7883 96.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 166.701 Å2
Baniso -1Baniso -2Baniso -3
1--5.81 Å2-0 Å20 Å2
2---1.32 Å2-0 Å2
3---7.13 Å2
Refinement stepCycle: 1 / Resolution: 3.75→74.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3878 0 0 0 3878
LS refinement shellResolution: 3.75→3.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 25 -
Rwork0.404 583 -
obs--99.67 %

+
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