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- PDB-2a1b: Carboxysome shell protein ccmK2 -

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Basic information

Entry
Database: PDB / ID: 2a1b
TitleCarboxysome shell protein ccmK2
ComponentsCarbon dioxide concentrating mechanism protein ccmK homolog 2
Keywordscarboxysome / cyclic hexamer / c6 point symmetry
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 CcmK2
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKerfeld, C.A. / Sawaya, M.R. / Tanaka, S. / Nguyen, C.V. / Phillips, M. / Beeby, M. / Yeates, T.O.
CitationJournal: Science / Year: 2005
Title: Protein structures forming the shell of primitive bacterial organelles
Authors: Kerfeld, C.A. / Sawaya, M.R. / Tanaka, S. / Nguyen, C.V. / Phillips, M. / Beeby, M. / Yeates, T.O.
History
DepositionJun 20, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbon dioxide concentrating mechanism protein ccmK homolog 2
B: Carbon dioxide concentrating mechanism protein ccmK homolog 2
C: Carbon dioxide concentrating mechanism protein ccmK homolog 2
D: Carbon dioxide concentrating mechanism protein ccmK homolog 2
E: Carbon dioxide concentrating mechanism protein ccmK homolog 2
F: Carbon dioxide concentrating mechanism protein ccmK homolog 2
G: Carbon dioxide concentrating mechanism protein ccmK homolog 2
H: Carbon dioxide concentrating mechanism protein ccmK homolog 2
I: Carbon dioxide concentrating mechanism protein ccmK homolog 2
J: Carbon dioxide concentrating mechanism protein ccmK homolog 2
K: Carbon dioxide concentrating mechanism protein ccmK homolog 2
L: Carbon dioxide concentrating mechanism protein ccmK homolog 2


Theoretical massNumber of molelcules
Total (without water)151,36012
Polymers151,36012
Non-polymers00
Water00
1
A: Carbon dioxide concentrating mechanism protein ccmK homolog 2
B: Carbon dioxide concentrating mechanism protein ccmK homolog 2
C: Carbon dioxide concentrating mechanism protein ccmK homolog 2
D: Carbon dioxide concentrating mechanism protein ccmK homolog 2
E: Carbon dioxide concentrating mechanism protein ccmK homolog 2
F: Carbon dioxide concentrating mechanism protein ccmK homolog 2


Theoretical massNumber of molelcules
Total (without water)75,6806
Polymers75,6806
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13240 Å2
ΔGint-92 kcal/mol
Surface area24430 Å2
MethodPISA
2
G: Carbon dioxide concentrating mechanism protein ccmK homolog 2
H: Carbon dioxide concentrating mechanism protein ccmK homolog 2
I: Carbon dioxide concentrating mechanism protein ccmK homolog 2
J: Carbon dioxide concentrating mechanism protein ccmK homolog 2
K: Carbon dioxide concentrating mechanism protein ccmK homolog 2
L: Carbon dioxide concentrating mechanism protein ccmK homolog 2


Theoretical massNumber of molelcules
Total (without water)75,6806
Polymers75,6806
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13380 Å2
ΔGint-93 kcal/mol
Surface area24300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.744, 179.987, 69.769
Angle α, β, γ (deg.)90.00, 119.98, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211
DetailsThe asymmetric unit contains two biological assemblies: a hexamer consisting of chains A,B,C,D,E,F, and a hexamer consisting of chains G,H,I,J,K,L.

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Components

#1: Protein
Carbon dioxide concentrating mechanism protein ccmK homolog 2 / ccmK2


Mass: 12613.297 Da / Num. of mol.: 12 / Mutation: E52G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Gene: ccmK2 / Plasmid: pET22B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold DE3 / References: UniProt: P72761

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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: 2.81 Å3/Da / Density % sol: 56.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: ammonium sulfate, methylpentanediol, dioxane, MES, 1,6 hexanediol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 8, 2004
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→100 Å / Num. all: 31983 / Num. obs: 31983 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: -0.8 Å2 / Rsym value: 0.12 / Net I/σ(I): 8.8
Reflection shellResolution: 2.9→3 Å / Redundancy: 2.3 % / Num. unique all: 2736 / Rsym value: 0.352 / % possible all: 83.5

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Processing

Software
NameVersionClassification
CrystalCleardata collection
SCALEPACKdata scaling
PHASERphasing
CNS1.1refinement
CrystalClear(MSC/RIGAKU)data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A10

2a10


Resolution: 2.9→89.99 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2141108.78 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Used twin operator -h,-k,h+l twin fraction 0.5
RfactorNum. reflection% reflectionSelection details
Rfree0.346 2863 9.1 %RANDOM
Rwork0.313 ---
all0.313 31634 --
obs0.313 31634 96 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 26.4503 Å2 / ksol: 0.379737 e/Å3
Displacement parametersBiso mean: 58.8 Å2
Baniso -1Baniso -2Baniso -3
1--37.12 Å20 Å2-11.11 Å2
2--67.7 Å20 Å2
3----30.59 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.77 Å0.76 Å
Luzzati d res low-5 Å
Luzzati sigma a1.02 Å1 Å
Refinement stepCycle: LAST / Resolution: 2.9→89.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9072 0 0 0 9072
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d1.02
LS refinement shellResolution: 2.9→3.08 Å / Total num. of bins used: 6
Num. reflection% reflection
Rfree358 7.5 %
Rwork4421 -
obs-87.9 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top

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