[English] 日本語
Yorodumi
- PDB-6uew: Rubisco / CsoS2 N-peptide complex responsible for alpha-carboxyso... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6uew
TitleRubisco / CsoS2 N-peptide complex responsible for alpha-carboxysome cargo loading
Components
  • Ribulose bisphosphate carboxylase large chain, CsoS2 N-peptide fusion
  • Ribulose bisphosphate carboxylase small chain
KeywordsPROTEIN BINDING / Rubisco / CsoS2 / carboxysome / phase separation
Function / homology
Function and homology information


carboxysome / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / monooxygenase activity / magnesium ion binding
Similarity search - Function
Ribulose bisphosphate carboxylase, small subunit / Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / Ribulose bisphosphate carboxylase small subunit, domain / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase large subunit, type I ...Ribulose bisphosphate carboxylase, small subunit / Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / Ribulose bisphosphate carboxylase small subunit, domain / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase large subunit, type I / Ribulose bisphosphate carboxylase, large chain, active site / Ribulose bisphosphate carboxylase large chain active site. / Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal / Ribulose bisphosphate carboxylase large chain, N-terminal domain / Ribulose bisphosphate carboxylase, large subunit, C-terminal / RuBisCO / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain superfamily / RuBisCO large subunit, N-terminal domain superfamily / Ribulose bisphosphate carboxylase large chain, catalytic domain / Alpha-Beta Plaits / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribulose bisphosphate carboxylase large chain / Ribulose bisphosphate carboxylase small subunit
Similarity search - Component
Biological speciesHalothiobacillus neapolitanus (bacteria)
Halothiobacillus neapolitanus c2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsOltrogge, L.M. / Savage, D.F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM129241 United States
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2020
Title: Multivalent interactions between CsoS2 and Rubisco mediate alpha-carboxysome formation.
Authors: Oltrogge, L.M. / Chaijarasphong, T. / Chen, A.W. / Bolin, E.R. / Marqusee, S. / Savage, D.F.
#1: Journal: Biorxiv / Year: 2019
Title: Alpha-carboxysome formation is mediated by the multivalent and disordered protein CsoS2
Authors: Oltrogge, L.M. / Chaijarasphong, T. / Chen, A.W. / Bolin, E.R. / Marqusee, S. / Savage, D.F.
History
DepositionSep 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 18, 2020Group: Database references / Category: citation / citation_author
Revision 1.3Mar 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ribulose bisphosphate carboxylase large chain, CsoS2 N-peptide fusion
B: Ribulose bisphosphate carboxylase small chain
C: Ribulose bisphosphate carboxylase large chain, CsoS2 N-peptide fusion
D: Ribulose bisphosphate carboxylase small chain
E: Ribulose bisphosphate carboxylase large chain, CsoS2 N-peptide fusion
F: Ribulose bisphosphate carboxylase small chain
G: Ribulose bisphosphate carboxylase large chain, CsoS2 N-peptide fusion
H: Ribulose bisphosphate carboxylase small chain


Theoretical massNumber of molelcules
Total (without water)276,6288
Polymers276,6288
Non-polymers00
Water12,034668
1
A: Ribulose bisphosphate carboxylase large chain, CsoS2 N-peptide fusion
B: Ribulose bisphosphate carboxylase small chain
C: Ribulose bisphosphate carboxylase large chain, CsoS2 N-peptide fusion
D: Ribulose bisphosphate carboxylase small chain
E: Ribulose bisphosphate carboxylase large chain, CsoS2 N-peptide fusion
F: Ribulose bisphosphate carboxylase small chain
G: Ribulose bisphosphate carboxylase large chain, CsoS2 N-peptide fusion
H: Ribulose bisphosphate carboxylase small chain

A: Ribulose bisphosphate carboxylase large chain, CsoS2 N-peptide fusion
B: Ribulose bisphosphate carboxylase small chain
C: Ribulose bisphosphate carboxylase large chain, CsoS2 N-peptide fusion
D: Ribulose bisphosphate carboxylase small chain
E: Ribulose bisphosphate carboxylase large chain, CsoS2 N-peptide fusion
F: Ribulose bisphosphate carboxylase small chain
G: Ribulose bisphosphate carboxylase large chain, CsoS2 N-peptide fusion
H: Ribulose bisphosphate carboxylase small chain


Theoretical massNumber of molelcules
Total (without water)553,25616
Polymers553,25616
Non-polymers00
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area87100 Å2
ΔGint-304 kcal/mol
Surface area124150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.831, 153.945, 108.063
Angle α, β, γ (deg.)90.000, 124.703, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11C-642-

HOH

21C-709-

HOH

31G-692-

HOH

41G-695-

HOH

51G-702-

HOH

61G-716-

HOH

-
Components

#1: Protein
Ribulose bisphosphate carboxylase large chain, CsoS2 N-peptide fusion / RuBisCO large subunit


Mass: 56290.449 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halothiobacillus neapolitanus (strain ATCC 23641 / c2) (bacteria), (gene. exp.) Halothiobacillus neapolitanus c2 (bacteria)
Strain: ATCC 23641 / c2 / Gene: cbbL, Hneap_0922 / Production host: Escherichia coli (E. coli)
References: UniProt: O85040, ribulose-bisphosphate carboxylase
#2: Protein
Ribulose bisphosphate carboxylase small chain / RuBisCO small subunit


Mass: 12866.575 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halothiobacillus neapolitanus (strain ATCC 23641 / c2) (bacteria)
Strain: ATCC 23641 / c2 / Gene: cbbS, rbcS, Hneap_0921 / Production host: Escherichia coli (E. coli)
References: UniProt: P45686, ribulose-bisphosphate carboxylase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 668 / 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: 2.35 Å3/Da / Density % sol: 47.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 400, magnesium chloride, HEPES

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 5, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11 Å / Relative weight: 1
ReflectionResolution: 2.4→104.1 Å / Num. obs: 90035 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 32.79 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1244 / Rpim(I) all: 0.05064 / Rrim(I) all: 0.1345 / Net I/σ(I): 12.84
Reflection shellResolution: 2.4→2.486 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.5876 / Mean I/σ(I) obs: 2.97 / Num. unique obs: 8960 / CC1/2: 0.92 / Rpim(I) all: 0.2497 / Rrim(I) all: 0.6396 / % possible all: 99.92

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Blu-Icedata collection
XDSdata reduction
Aimlessdata scaling
Coot0.8.9model building
PHENIX1.13_2998phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SVD

1svd


Resolution: 2.4→104.08 Å / SU ML: 0.312 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.2779
RfactorNum. reflection% reflection
Rfree0.2589 1429 1.59 %
Rwork0.1878 --
obs0.189 89949 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 41.8 Å2
Refinement stepCycle: LAST / Resolution: 2.4→104.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17636 0 0 668 18304
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007818090
X-RAY DIFFRACTIONf_angle_d0.880924518
X-RAY DIFFRACTIONf_chiral_restr0.05012566
X-RAY DIFFRACTIONf_plane_restr0.00583205
X-RAY DIFFRACTIONf_dihedral_angle_d7.05510606
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.490.31471440.23568810X-RAY DIFFRACTION99.88
2.49-2.590.38941450.23618788X-RAY DIFFRACTION99.81
2.59-2.70.33411400.22578835X-RAY DIFFRACTION99.89
2.7-2.850.28831390.21488843X-RAY DIFFRACTION99.96
2.85-3.020.29681370.21268852X-RAY DIFFRACTION99.92
3.02-3.260.24741490.20798814X-RAY DIFFRACTION99.94
3.26-3.590.25251430.18568884X-RAY DIFFRACTION99.98
3.59-4.10.26691480.16778858X-RAY DIFFRACTION99.97
4.1-5.170.2081400.15248864X-RAY DIFFRACTION99.86
5.17-104.080.21971440.17668972X-RAY DIFFRACTION99.7

+
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