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- PDB-6scr: Structure of CcmK4 from Synechocystis sp. PCC6803 -

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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 / 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 ...Carboxysome shell protein CcmK / BMC (bacterial microcompartment) domain / 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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


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


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.13 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

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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

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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

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