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- PDB-3cim: Carboxysome shell protein, CcmK2 C-terminal deletion mutant -

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Basic information

Entry
Database: PDB / ID: 3cim
TitleCarboxysome shell protein, CcmK2 C-terminal deletion mutant
ComponentsCarbon dioxide-concentrating mechanism protein ccmK homolog 2
KeywordsSTRUCTURAL PROTEIN / hexamer
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 CcmK2
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å
AuthorsTanaka, S. / Sawaya, M.R. / Yeates, T.O.
CitationJournal: Protein Sci. / Year: 2009
Title: Insights from multiple structures of the shell proteins from the beta-carboxysome.
Authors: Tanaka, S. / Sawaya, M.R. / Phillips, M. / Yeates, T.O.
History
DepositionMar 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3088
Polymers31,8393
Non-polymers4685
Water6,233346
1
B: Carbon dioxide-concentrating mechanism protein ccmK homolog 2
C: Carbon dioxide-concentrating mechanism protein ccmK homolog 2
hetero molecules

B: Carbon dioxide-concentrating mechanism protein ccmK homolog 2
C: Carbon dioxide-concentrating mechanism protein ccmK homolog 2
hetero molecules

B: Carbon dioxide-concentrating mechanism protein ccmK homolog 2
C: Carbon dioxide-concentrating mechanism protein ccmK homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,51915
Polymers63,6796
Non-polymers8419
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area14050 Å2
ΔGint-114.7 kcal/mol
Surface area21060 Å2
MethodPISA
2
A: Carbon dioxide-concentrating mechanism protein ccmK homolog 2
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)64,80818
Polymers63,6796
Non-polymers1,12912
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
Buried area13540 Å2
ΔGint-79.9 kcal/mol
Surface area21160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.802, 120.802, 29.235
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6

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Components

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


Mass: 10613.096 Da / Num. of mol.: 3 / Fragment: Residues 1-91
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Gene: ccmK2 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Gold / References: UniProt: P72761
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H2O

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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: 1.93 Å3/Da / Density % sol: 36.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 0.1M CHES, 1.26M ammonium sulfate, 0.15M NaCl, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.979 Å
DetectorType: ADXV quantum Q315 / Detector: CCD / Date: Nov 8, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.3→90 Å / Num. obs: 58974 / % possible obs: 97.4 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.076 / Χ2: 1.006 / Net I/σ(I): 11.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.3-1.353.10.58659571.078199.4
1.35-1.43.10.36359700.931199.2
1.4-1.463.10.31559291.046198.9
1.46-1.543.10.20959621.001198.8
1.54-1.643.20.1459270.976199.1
1.64-1.763.30.10959420.99199
1.76-1.943.20.10559311.01197.7
1.94-2.223.40.07259851.002198.6
2.22-2.83.60.06359971.057198.6
2.8-903.50.05953740.965185.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å52.31 Å
Translation3.5 Å52.31 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→52.34 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.065 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.065 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.222 2978 5.1 %RANDOM
Rwork0.171 ---
obs0.173 58523 96.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.636 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.3→52.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2092 0 28 346 2466
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0212316
X-RAY DIFFRACTIONr_angle_refined_deg1.4171.9553185
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2125338
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.98222.47393
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.13215394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.911523
X-RAY DIFFRACTIONr_chiral_restr0.0940.2384
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211742
X-RAY DIFFRACTIONr_mcbond_it3.25221488
X-RAY DIFFRACTIONr_mcangle_it4.24432437
X-RAY DIFFRACTIONr_scbond_it3.862828
X-RAY DIFFRACTIONr_scangle_it5.5313717
X-RAY DIFFRACTIONr_rigid_bond_restr2.87132316
X-RAY DIFFRACTIONr_sphericity_free11.4223346
X-RAY DIFFRACTIONr_sphericity_bonded6.68632259
LS refinement shellResolution: 1.301→1.335 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 216 -
Rwork0.306 3887 -
all-4103 -
obs--91.91 %

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