[English] 日本語
Yorodumi
- PDB-9iv7: Crystal structure of CcmS-CcmK1-CcmK2 complex from Synechocystis ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9iv7
TitleCrystal structure of CcmS-CcmK1-CcmK2 complex from Synechocystis sp. PCC 6803
Components
  • Carboxysome shell protein CcmK1
  • Carboxysome shell protein CcmK2
  • Slr1911 protein
KeywordsCHAPERONE / cyanobacteria / CO2-concentrating mechanism / carboxysome assembly / shell proteins / Synechocystis sp. PCC 6803
Function / homology
Function and homology information


structural constituent of carboxysome shell / carboxysome / carbon fixation / photosynthesis
Similarity search - Function
Carboxysome shell protein CcmK / Bacterial microcompartments protein, conserved site / Bacterial microcompartment (BMC) domain signature. / CcmK/CsoS1, bacterial microcompartment domain / : / Bacterial microcompartment (BMC) domain profile. / BMC domain / Bacterial microcompartment domain / BMC / CcmK-like superfamily
Similarity search - Domain/homology
D(-)-TARTARIC ACID / Carboxysome shell protein CcmK1 / Carboxysome shell protein CcmK2 / Slr1911 protein
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 substr. Kazusa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLi, J. / Deng, J.X. / Jiang, Y.L. / Zhou, C.Z.
Funding support China, 7items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171198 China
National Natural Science Foundation of China (NSFC)32241025 China
Anhui Provincial Key Research and Development Project2022l07020034 China
Chaohu Lake Biological Resource Investigation and Research Project2020-340181-77-01-037328 China
USTC Research Funds of the Double First-Class InitiativeYD9100002023 China
Youth Innovation Promotion Association of the Chinese Academy of Sciences2020452 China
Chinese Academy of SciencesXDA24020302 China
CitationJournal: To Be Published
Title: Assembly mechanism of beta-carboxysome shell mediated by the chaperone CcmS
Authors: Li, J. / Deng, J.X. / Chen, X. / Li, B. / Li, B.R. / Zhu, Z.L. / Liu, J.X. / Zhou, C.Z. / Jiang, Y.L. / Chen, Y.X. / Mi, H.L.
History
DepositionJul 23, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Slr1911 protein
B: Carboxysome shell protein CcmK1
C: Carboxysome shell protein CcmK1
D: Carboxysome shell protein CcmK2
E: Carboxysome shell protein CcmK2
F: Carboxysome shell protein CcmK1
G: Slr1911 protein
H: Carboxysome shell protein CcmK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,3629
Polymers103,2128
Non-polymers1501
Water6,828379
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19400 Å2
ΔGint-108 kcal/mol
Surface area34970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.931, 58.039, 188.768
Angle α, β, γ (deg.)90.00, 105.48, 90.00
Int Tables number5
Space group name H-MI121

-
Components

#1: Protein Slr1911 protein


Mass: 16227.491 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Strain: ATCC 27184 / PCC 6803 / Kazusa / Gene: slr1911 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): BL21 / References: UniProt: P73106
#2: Protein
Carboxysome shell protein CcmK1 / Carbon dioxide-concentrating mechanism protein CcmK1


Mass: 12115.935 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Strain: ATCC 27184 / PCC 6803 / Kazusa / Gene: ccmK1, sll1029 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): BL21 / References: UniProt: P72760
#3: Protein Carboxysome shell protein CcmK2 / Carbon dioxide-concentrating mechanism protein CcmK2


Mass: 11146.661 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Strain: ATCC 27184 / PCC 6803 / Kazusa / Gene: ccmK2, sll1028 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): BL21 / References: UniProt: P72761
#4: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H6O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.42 Å3/Da / Density % sol: 64.06 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris (pH 8.5) and 0.7 M ammonium tartrate dibasic

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5406 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jul 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 2.5→13.24 Å / Num. obs: 48376 / % possible obs: 98.9 % / Redundancy: 3.2 % / Rpim(I) all: 0.064 / Net I/σ(I): 8.1
Reflection shellResolution: 2.5→2.58 Å / Rmerge(I) obs: 0.014 / Num. unique obs: 4388

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→13.24 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2406 2412 5 %
Rwork0.2146 --
obs0.216 48254 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→13.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6684 0 10 379 7073
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.472
X-RAY DIFFRACTIONf_dihedral_angle_d12.2282502
X-RAY DIFFRACTIONf_chiral_restr0.0431078
X-RAY DIFFRACTIONf_plane_restr0.0041198
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.550.3991540.31522642X-RAY DIFFRACTION98
2.55-2.610.3211170.30882697X-RAY DIFFRACTION99
2.61-2.670.34991280.30112658X-RAY DIFFRACTION99
2.67-2.730.29941290.27182684X-RAY DIFFRACTION99
2.73-2.810.32251450.26922662X-RAY DIFFRACTION100
2.81-2.890.30781390.26772730X-RAY DIFFRACTION100
2.89-2.980.30781340.25832674X-RAY DIFFRACTION100
2.98-3.080.25981650.24012684X-RAY DIFFRACTION100
3.08-3.210.27051430.24332646X-RAY DIFFRACTION100
3.21-3.350.25221520.24572705X-RAY DIFFRACTION100
3.35-3.520.28181430.22322702X-RAY DIFFRACTION100
3.52-3.740.21681380.20142708X-RAY DIFFRACTION100
3.74-4.020.20971370.19192729X-RAY DIFFRACTION99
4.02-4.410.20471420.17712694X-RAY DIFFRACTION99
4.41-5.020.18611540.16592693X-RAY DIFFRACTION99
5.02-6.210.19221500.18762738X-RAY DIFFRACTION100
6.21-13.240.17671420.15542796X-RAY DIFFRACTION99

+
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