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- PDB-4ox6: Structure of Synechococcus elongatus PCC 7942 CcmK4 -

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Basic information

Entry
Database: PDB / ID: 4ox6
TitleStructure of Synechococcus elongatus PCC 7942 CcmK4
ComponentsCarbon dioxide concentrating mechanism protein CcmK
KeywordsSTRUCTURAL PROTEIN / Bacterial Microcompartment
Function / homology
Function and homology information


BMC (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 CcmK4
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3367 Å
AuthorsSutter, M. / Kinney, J.N. / Cai, F. / Kerfeld, C.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-AC02-05CH11231 United States
CitationJournal: Acs Synth Biol / Year: 2015
Title: Engineering bacterial microcompartment shells: chimeric shell proteins and chimeric carboxysome shells.
Authors: Cai, F. / Sutter, M. / Bernstein, S.L. / Kinney, J.N. / Kerfeld, C.A.
History
DepositionFeb 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2015Group: Database references
Revision 1.2Sep 6, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_validate_close_contact
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: 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 / refine_hist
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
B: Carbon dioxide concentrating mechanism protein CcmK


Theoretical massNumber of molelcules
Total (without water)27,1552
Polymers27,1552
Non-polymers00
Water1,51384
1
A: Carbon dioxide concentrating mechanism protein CcmK
B: Carbon dioxide concentrating mechanism protein CcmK

A: Carbon dioxide concentrating mechanism protein CcmK
B: Carbon dioxide concentrating mechanism protein CcmK

A: Carbon dioxide concentrating mechanism protein CcmK
B: Carbon dioxide concentrating mechanism protein CcmK


Theoretical massNumber of molelcules
Total (without water)81,4646
Polymers81,4646
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area12830 Å2
ΔGint-100 kcal/mol
Surface area21540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.452, 67.452, 63.351
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
DetailsOligomeric state confirmed by gel filtration

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Components

#1: Protein Carbon dioxide concentrating mechanism protein CcmK


Mass: 13577.287 Da / Num. of mol.: 2 / Fragment: UNP Residues 1-113
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (bacteria) / Strain: PCC 7942 / Gene: Synpcc7942_0285 / Production host: Escherichia coli (E. coli) / References: UniProt: Q31RK2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 1.53 Å3/Da / Density % sol: 19.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MgCl2, 0.1 M sodium citrate pH 5.0, 15 % (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9762 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 6, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.3367→33.726 Å / Num. obs: 34786 / % possible obs: 93.8 % / Observed criterion σ(I): -3 / Redundancy: 9.2 % / Rmerge(I) obs: 0.0446 / Net I/σ(I): 28.33
Reflection shellResolution: 1.3367→1.38 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.723 / Mean I/σ(I) obs: 1.63 / % possible all: 63.4

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2A10

2a10


Resolution: 1.3367→33.726 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1894 1995 5.75 %
Rwork0.1668 --
obs0.1682 34725 93.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3367→33.726 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1453 0 0 84 1537
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.021483
X-RAY DIFFRACTIONf_angle_d1.7922013
X-RAY DIFFRACTIONf_dihedral_angle_d13.7544
X-RAY DIFFRACTIONf_chiral_restr0.118229
X-RAY DIFFRACTIONf_plane_restr0.011264
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3367-1.37020.3893900.36751487X-RAY DIFFRACTION60
1.3702-1.40720.30811160.27361883X-RAY DIFFRACTION76
1.4072-1.44860.29281340.22552166X-RAY DIFFRACTION87
1.4486-1.49540.21471400.19692308X-RAY DIFFRACTION93
1.4954-1.54880.23471470.1912411X-RAY DIFFRACTION97
1.5488-1.61080.21391520.1672469X-RAY DIFFRACTION100
1.6108-1.68420.22481540.15042493X-RAY DIFFRACTION100
1.6842-1.77290.16921570.15362483X-RAY DIFFRACTION100
1.7729-1.8840.18751490.15552479X-RAY DIFFRACTION100
1.884-2.02950.17031460.14492478X-RAY DIFFRACTION100
2.0295-2.23370.17351450.14592509X-RAY DIFFRACTION100
2.2337-2.55680.18871550.15642511X-RAY DIFFRACTION100
2.5568-3.22090.17741530.16692507X-RAY DIFFRACTION100
3.2209-33.73670.16251570.16222546X-RAY DIFFRACTION100

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