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- PDB-9iv7: Crystal structure of CcmS-CcmK1-CcmK2 complex from Synechocystis ... -

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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: New Phytol. / Year: 2025
Title: Assembly mechanism of the 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. / Chen, Y. / Mi, H. / Zhou, C.Z. / Jiang, Y.L.
History
DepositionJul 23, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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