[English] 日本語
Yorodumi
- PDB-6jy5: Structure of CsoS4B from Halothiobacillus neapolitanus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6jy5
TitleStructure of CsoS4B from Halothiobacillus neapolitanus
ComponentsUnidentified carboxysome polypeptide
KeywordsSTRUCTURAL PROTEIN / carboxysome shell protein / pentameric protein
Function / homology
Function and homology information


carboxysome / carbon fixation
Similarity search - Function
Carboxysome shell vertex protein CsoS4B / EutN/Ccml / Ethanolamine utilization protein EutN/carboxysome shell vertex protein CcmL / EutN/Ccml superfamily / Ethanolamine utilisation protein EutN/carboxysome / Bacterial microcompartment vertex (BMV) domain profile. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Carboxysome shell vertex protein CsoS4B
Similarity search - Component
Biological speciesHalothiobacillus neapolitanus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsZhao, Y.Y. / Jiang, Y.L. / Chen, Y. / Zhou, C.Z. / Li, Q.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31630001 China
National Natural Science Foundation of China31621002 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2019
Title: Crystal structure of pentameric shell protein CsoS4B of Halothiobacillus neapolitanus alpha-carboxysome.
Authors: Zhao, Y.Y. / Jiang, Y.L. / Chen, Y. / Zhou, C.Z. / Li, Q.
History
DepositionApr 26, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 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
D: Unidentified carboxysome polypeptide
A: Unidentified carboxysome polypeptide
B: Unidentified carboxysome polypeptide
C: Unidentified carboxysome polypeptide
E: Unidentified carboxysome polypeptide


Theoretical massNumber of molelcules
Total (without water)46,5895
Polymers46,5895
Non-polymers00
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9190 Å2
ΔGint-50 kcal/mol
Surface area17300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.337, 68.434, 70.907
Angle α, β, γ (deg.)90.00, 124.42, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Unidentified carboxysome polypeptide / microcompartment protein


Mass: 9317.740 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halothiobacillus neapolitanus (bacteria)
Plasmid: pET-29a-derived / Production host: Escherichia coli (E. coli) / References: UniProt: O85044
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.17 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% polyethylene glycol 400, 0.2 M Li2SO4 and 0.1 M sodium cacodylate pH 6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 20226 / % possible obs: 98.1 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.187 / Rsym value: 0.187 / Net I/σ(I): 10.259
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.678 / Mean I/σ(I) obs: 3.41 / Num. unique obs: 2011 / Rsym value: 0.678 / % possible all: 98.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2rcf

2rcf


Resolution: 2.15→40.18 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.374 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.252 / ESU R Free: 0.201 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2266 1013 5 %RANDOM
Rwork0.16969 ---
obs0.17248 19213 97.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.206 Å2
Baniso -1Baniso -2Baniso -3
1--1.49 Å20 Å20.36 Å2
2---0.53 Å2-0 Å2
3---0.79 Å2
Refinement stepCycle: 1 / Resolution: 2.15→40.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2899 0 0 190 3089
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132936
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172911
X-RAY DIFFRACTIONr_angle_refined_deg1.5241.6313965
X-RAY DIFFRACTIONr_angle_other_deg1.2611.5816698
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6095379
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.35419.855138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.95815518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6551529
X-RAY DIFFRACTIONr_chiral_restr0.0640.2413
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023243
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02616
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4953.0981537
X-RAY DIFFRACTIONr_mcbond_other2.4953.0971536
X-RAY DIFFRACTIONr_mcangle_it3.5944.6291909
X-RAY DIFFRACTIONr_mcangle_other3.5934.6291910
X-RAY DIFFRACTIONr_scbond_it3.6433.6791399
X-RAY DIFFRACTIONr_scbond_other3.6333.6761397
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.545.3052056
X-RAY DIFFRACTIONr_long_range_B_refined7.14137.0842986
X-RAY DIFFRACTIONr_long_range_B_other7.1236.8312951
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.158→2.214 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 59 -
Rwork0.197 1298 -
obs--86.82 %

+
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