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- PDB-3dnc: Carboxysome shell protein, CcmK2 C-terminal deletion mutant, with... -

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Basic information

Entry
Database: PDB / ID: 3dnc
TitleCarboxysome shell protein, CcmK2 C-terminal deletion mutant, with a closer spacing between hexamers
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 / 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 / molecular replacement / Resolution: 2.05 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
DepositionJul 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Carbon dioxide-concentrating mechanism protein ccmK homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8974
Polymers10,6131
Non-polymers2843
Water72140
1
A: Carbon dioxide-concentrating mechanism protein ccmK homolog 2
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)65,38424
Polymers63,6796
Non-polymers1,70518
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 area12940 Å2
ΔGint-182 kcal/mol
Surface area19320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.362, 67.362, 29.034
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-100-

SO4

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Components

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


Mass: 10613.096 Da / Num. of mol.: 1 / Fragment: C-terminal (UNP residues 92-103) deletion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Gene: ccmK2, sll1028 / 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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 1.79 Å3/Da / Density % sol: 31.35 %
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: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 9, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→80 Å / Num. obs: 4371 / % possible obs: 89.2 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.152 / Χ2: 1.009 / Net I/σ(I): 7.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.05-2.127.40.4564690.943199.8
2.12-2.217.50.3544900.9921100
2.21-2.317.50.3024831.0031100
2.31-2.437.40.2394870.998199.6
2.43-2.587.30.1984731.029199
2.58-2.787.20.1664781.092198.6
2.78-3.0670.1364711.032194.4
3.06-3.516.60.1224040.997183.6
3.51-4.426.40.1243071.02161.6
4.42-805.90.1223090.965158.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2A1B

2a1b


Resolution: 2.05→58.32 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.884 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.803 / SU B: 11.831 / SU ML: 0.148 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.365 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.278 204 4.7 %RANDOM
Rwork0.222 ---
obs0.224 4369 89.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 118.6 Å2 / Biso mean: 51.995 Å2 / Biso min: 26.63 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.04 Å20 Å2
2--0.08 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.05→58.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms661 0 16 40 717
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.022694
X-RAY DIFFRACTIONr_bond_other_d0.0010.02457
X-RAY DIFFRACTIONr_angle_refined_deg1.0221.983944
X-RAY DIFFRACTIONr_angle_other_deg0.89131118
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.935593
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.37922.69226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.08115115
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.295157
X-RAY DIFFRACTIONr_chiral_restr0.0590.2115
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.02766
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02133
X-RAY DIFFRACTIONr_mcbond_it1.0912449
X-RAY DIFFRACTIONr_mcbond_other0.2112187
X-RAY DIFFRACTIONr_mcangle_it1.7683727
X-RAY DIFFRACTIONr_scbond_it1.22245
X-RAY DIFFRACTIONr_scangle_it1.893215
LS refinement shellResolution: 2.047→2.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 19 -
Rwork0.299 339 -
all-358 -
obs--99.72 %
Refinement TLS params.Method: refined / Origin x: 19.2433 Å / Origin y: -9.4293 Å / Origin z: -9.3427 Å
111213212223313233
T-0.248 Å2-0.0257 Å20.0023 Å2--0.2054 Å2-0.0049 Å2---0.3014 Å2
L1.3037 °20.2954 °2-0.2164 °2-2.6661 °2-0.0049 °2--0.0367 °2
S-0.0673 Å °-0.0586 Å °-0.0049 Å °0.0865 Å °0.0634 Å °0.0697 Å °0.024 Å °0.0724 Å °0.0039 Å °

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