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- PDB-5vgu: Structure of Halothece sp. PCC 7418 CcmK4 -

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Basic information

Entry
Database: PDB / ID: 5vgu
TitleStructure of Halothece sp. PCC 7418 CcmK4
ComponentsMicrocompartments proteinBacterial microcompartment
KeywordsSTRUCTURAL PROTEIN / Bacterial Microcompartment
Function / homology
Function and homology information


carboxysome / carbon fixation / photosynthesis
Similarity search - Function
BMC (bacterial microcompartment) domain / 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 speciesHalothece sp. PCC 7418 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.80719333143 Å
AuthorsSutter, M. / Sommer, M. / Kerfeld, C.A.
CitationJournal: Plant Physiol. / Year: 2019
Title: Heterohexamers Formed by CcmK3 and CcmK4 Increase the Complexity of Beta Carboxysome Shells.
Authors: Sommer, M. / Sutter, M. / Gupta, S. / Kirst, H. / Turmo, A. / Lechno-Yossef, S. / Burton, R.L. / Saechao, C. / Sloan, N.B. / Cheng, X. / Chan, L.G. / Petzold, C.J. / Fuentes-Cabrera, M. / ...Authors: Sommer, M. / Sutter, M. / Gupta, S. / Kirst, H. / Turmo, A. / Lechno-Yossef, S. / Burton, R.L. / Saechao, C. / Sloan, N.B. / Cheng, X. / Chan, L.G. / Petzold, C.J. / Fuentes-Cabrera, M. / Ralston, C.Y. / Kerfeld, C.A.
History
DepositionApr 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Microcompartments protein
B: Microcompartments protein
C: Microcompartments protein
D: Microcompartments protein
E: Microcompartments protein
F: Microcompartments protein


Theoretical massNumber of molelcules
Total (without water)81,9576
Polymers81,9576
Non-polymers00
Water6,053336
1
A: Microcompartments protein
B: Microcompartments protein
C: Microcompartments protein

A: Microcompartments protein
B: Microcompartments protein
C: Microcompartments protein


Theoretical massNumber of molelcules
Total (without water)81,9576
Polymers81,9576
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area13980 Å2
ΔGint-109 kcal/mol
Surface area22930 Å2
MethodPISA
2
D: Microcompartments protein
E: Microcompartments protein
F: Microcompartments protein

D: Microcompartments protein
E: Microcompartments protein
F: Microcompartments protein


Theoretical massNumber of molelcules
Total (without water)81,9576
Polymers81,9576
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area13920 Å2
ΔGint-109 kcal/mol
Surface area22660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.957, 93.997, 72.815
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 2 - 102 / Label seq-ID: 2 - 102

Dom-IDComponent-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain 'A' and resid 2 through 102)AA
22chain 'B'BB
33(chain 'C' and resid 2 through 102)CC
44(chain 'D' and resid 2 through 102)DD
55chain 'E'EE
66(chain 'F' and resid 2 through 102)FF

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Components

#1: Protein
Microcompartments protein / Bacterial microcompartment


Mass: 13659.525 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halothece sp. PCC 7418 (bacteria) / Strain: PCC 7418 / Gene: PCC7418_0347 / Production host: Escherichia coli (E. coli) / References: UniProt: K9Y6N7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 336 / 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: 2.09 Å3/Da / Density % sol: 41.06 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 40% MPD, 0.1 M HEPES pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.976484 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976484 Å / Relative weight: 1
ReflectionResolution: 1.807→44.13 Å / Num. obs: 63270 / % possible obs: 99.7 % / Redundancy: 14.7 % / Biso Wilson estimate: 20.5573020423 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Net I/σ(I): 23.2
Reflection shellResolution: 1.807→1.9 Å / Redundancy: 14.8 % / Rmerge(I) obs: 0.856 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 9046 / CC1/2: 0.92 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A10

2a10


Resolution: 1.80719333143→44.1285113667 Å / SU ML: 0.17406738915 / Cross valid method: FREE R-VALUE / σ(F): 1.34642796485 / Phase error: 18.0108419537
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.18502135184 2000 3.16475726312 %random
Rwork0.157662992393 61196 --
obs0.158508434874 63196 99.5463423855 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.829036037 Å2
Refinement stepCycle: LAST / Resolution: 1.80719333143→44.1285113667 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4654 0 0 336 4990
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008737113077994732
X-RAY DIFFRACTIONf_angle_d0.9104709967846426
X-RAY DIFFRACTIONf_chiral_restr0.0593329428849760
X-RAY DIFFRACTIONf_plane_restr0.00781108479326826
X-RAY DIFFRACTIONf_dihedral_angle_d12.15059922142828
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8072-1.85240.3027387993021380.2468719118824249X-RAY DIFFRACTION98.5178531327
1.8524-1.90250.2303691881311390.2006318381164302X-RAY DIFFRACTION99.1073421111
1.9025-1.95850.1831169644841380.1771907452034316X-RAY DIFFRACTION99.1540516474
1.9585-2.02170.1829188588461460.1630606960254266X-RAY DIFFRACTION98.9681471512
2.0217-2.09390.2089748089241370.1619184726064342X-RAY DIFFRACTION99.4891159485
2.0939-2.17780.1929963566411440.1518227642474321X-RAY DIFFRACTION99.68743023
2.1778-2.27690.1919574507221350.1471377642664358X-RAY DIFFRACTION99.5347806823
2.2769-2.39690.1743516666931470.14901220994323X-RAY DIFFRACTION99.8213488164
2.3969-2.54710.1898846424591430.1435536693094384X-RAY DIFFRACTION99.7795900375
2.5471-2.74370.1727580223771480.1539404435444379X-RAY DIFFRACTION99.8896734334
2.7437-3.01970.2042296311211390.1541029803534422X-RAY DIFFRACTION99.9561691869
3.0197-3.45660.1843932828511460.154664745774410X-RAY DIFFRACTION99.9780557384
3.4566-4.35430.1617822656371440.1442304736334476X-RAY DIFFRACTION100
4.3543-44.14170.1755545530241560.1641874378944648X-RAY DIFFRACTION99.7508305648

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