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- PDB-9iur: Crystal structure of CcmS from Synechocystis sp. PCC 6803 -

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Entry
Database: PDB / ID: 9iur
TitleCrystal structure of CcmS from Synechocystis sp. PCC 6803
ComponentsSlr1911 protein
KeywordsCHAPERONE / cyanobacteria / CO2-concentrating mechanism / carboxysome assembly / shell proteins
Function / homologyIODIDE ION / Slr1911 protein
Function and homology information
Biological speciesSynechocystis sp. PCC 6803 substr. Kazusa (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.35 Å
AuthorsLi, J. / Deng, J.X. / Jiang, Y.L. / Zhou, C.Z.
Funding support China, 7items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDA24020302 China
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
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 22, 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

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Assembly

Deposited unit
A: Slr1911 protein
B: Slr1911 protein
C: Slr1911 protein
D: Slr1911 protein
E: Slr1911 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,27325
Polymers78,7355
Non-polymers2,53820
Water3,783210
1
A: Slr1911 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5087
Polymers15,7471
Non-polymers7616
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Slr1911 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2555
Polymers15,7471
Non-polymers5084
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Slr1911 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0013
Polymers15,7471
Non-polymers2542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Slr1911 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8742
Polymers15,7471
Non-polymers1271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Slr1911 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6358
Polymers15,7471
Non-polymers8887
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.963, 132.963, 38.085
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: -x,-y,z+1/2

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Components

#1: Protein
Slr1911 protein


Mass: 15746.946 Da / Num. of mol.: 5
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: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.05 Å3/Da / Density % sol: 39.97 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris (pH 7.5), 25% PEG 6000, and 0.6 M LiCl

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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: Apr 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 2.35→13.04 Å / Num. obs: 28219 / % possible obs: 99.4 % / Redundancy: 4.6 % / CC1/2: 0.994 / Net I/σ(I): 13.6
Reflection shellResolution: 2.35→2.44 Å / Mean I/σ(I) obs: 4.6 / Num. unique obs: 2948 / CC1/2: 0.562 / Rpim(I) all: 0.092 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.35→13.04 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2719 1401 4.97 %
Rwork0.2325 --
obs0.2345 28208 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→13.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5190 0 20 210 5420
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.489
X-RAY DIFFRACTIONf_dihedral_angle_d14.4051955
X-RAY DIFFRACTIONf_chiral_restr0.04775
X-RAY DIFFRACTIONf_plane_restr0.004940
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.430.37821240.30292661X-RAY DIFFRACTION100
2.43-2.530.35571490.28642647X-RAY DIFFRACTION100
2.53-2.640.33821460.27822620X-RAY DIFFRACTION100
2.64-2.780.31511390.28292689X-RAY DIFFRACTION100
2.78-2.950.31771170.27712678X-RAY DIFFRACTION100
2.96-3.180.29331470.24622687X-RAY DIFFRACTION100
3.18-3.490.26891450.22392662X-RAY DIFFRACTION100
3.5-3.990.25761350.19852671X-RAY DIFFRACTION100
3.99-4.980.21351420.19442710X-RAY DIFFRACTION100
4.98-13.040.24091570.21992782X-RAY DIFFRACTION100

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