[English] 日本語
Yorodumi
- PDB-6scr: Structure of CcmK4 from Synechocystis sp. PCC6803 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6scr
TitleStructure of CcmK4 from Synechocystis sp. PCC6803
ComponentsCarbon dioxide-concentrating mechanism protein CcmK homolog 4
KeywordsSTRUCTURAL PROTEIN / bacterial micro-compartment / carboxysome / CcmK4 / 2D assembly
Function / homology
Function and homology information


structural constituent of carboxysome shell / carboxysome / carbon fixation / photosynthesis
Similarity search - Function
Carboxysome shell protein CcmK / BMC (bacterial microcompartment) domain / CcmK/CsoS1, bacterial microcompartment domain / Bacterial microcompartments protein, conserved site / Bacterial microcompartment (BMC) domain signature. / Bacterial microcompartment (BMC) domain profile. / BMC domain / Bacterial microcompartment domain / CcmK-like superfamily / BMC ...Carboxysome shell protein CcmK / BMC (bacterial microcompartment) domain / CcmK/CsoS1, bacterial microcompartment domain / Bacterial microcompartments protein, conserved site / Bacterial microcompartment (BMC) domain signature. / Bacterial microcompartment (BMC) domain profile. / BMC domain / Bacterial microcompartment domain / CcmK-like superfamily / BMC / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Carboxysome shell protein CcmK4
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMaveyraud, L. / Garcia-Alles, L.F. / Mourey, L.
CitationJournal: Plos One / Year: 2019
Title: Occurrence and stability of hetero-hexamer associations formed by beta-carboxysome CcmK shell components.
Authors: Garcia-Alles, L.F. / Root, K. / Maveyraud, L. / Aubry, N. / Lesniewska, E. / Mourey, L. / Zenobi, R. / Truan, G.
History
DepositionJul 25, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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: Carbon dioxide-concentrating mechanism protein CcmK homolog 4
B: Carbon dioxide-concentrating mechanism protein CcmK homolog 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7903
Polymers27,7282
Non-polymers621
Water2,648147
1
A: Carbon dioxide-concentrating mechanism protein CcmK homolog 4
B: Carbon dioxide-concentrating mechanism protein CcmK homolog 4
hetero molecules

A: Carbon dioxide-concentrating mechanism protein CcmK homolog 4
B: Carbon dioxide-concentrating mechanism protein CcmK homolog 4
hetero molecules

A: Carbon dioxide-concentrating mechanism protein CcmK homolog 4
B: Carbon dioxide-concentrating mechanism protein CcmK homolog 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,3699
Polymers83,1836
Non-polymers1863
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area13270 Å2
ΔGint-99 kcal/mol
Surface area22240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.681, 70.681, 64.787
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11A-360-

HOH

-
Components

#1: Protein Carbon dioxide-concentrating mechanism protein CcmK homolog 4


Mass: 13863.758 Da / Num. of mol.: 2 / Mutation: MAHHHHASGENLYFQGAMA is an added Nterminal tag
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / Gene: ccmK4, slr1839 / Plasmid: pET-26b
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P73407
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.13 Å3/Da / Density % sol: 42.27 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 22 % (w/v) PEG 4000 0.2 M ammonium sulfate 0.1 M sodium acetate at pH 4.6

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.8→61.21 Å / Num. obs: 17065 / % possible obs: 99.6 % / Redundancy: 10.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.031 / Rrim(I) all: 0.1 / Χ2: 0.97 / Net I/σ(I): 14.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.8410.51.2821.99940.8470.5731.3480.9899.7
9-61.218.90.03743.41490.9990.0170.0390.9198.2

-
Processing

Software
NameClassification
Cootmodel building
PHENIXrefinement
REFMACrefinement
PHASERphasing
TRUNCATEdata reduction
XSCALEdata scaling
Aimlessdata scaling
XDSdata scaling
EDNAdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A18

2a18


Resolution: 1.8→61.2 Å / Cross valid method: FREE R-VALUE / Phase error: 27.08
RfactorNum. reflection% reflectionSelection details
Rfree0.1924 869 5.1 %random selection
Rwork0.171 ---
obs0.1721 17024 99.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 32.7 Å2
Refinement stepCycle: LAST / Resolution: 1.8→61.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1509 0 4 147 1660

+
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