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- PDB-5v75: Structure of Haliangium ochraceum BMC-T HO-5816 -

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Basic information

Entry
Database: PDB / ID: 5v75
TitleStructure of Haliangium ochraceum BMC-T HO-5816
ComponentsMicrocompartments protein
KeywordsSTRUCTURAL PROTEIN / BACTERIAL MICROCOMPARTMENTS
Function / homology
Function and homology information


bacterial microcompartment
Similarity search - Function
Bacterial microcompartment (BMC) circularly permuted domain / Bacterial microcompartment (BMC) circularly permuted domain profile. / BMC (bacterial microcompartment) domain / BMC domain / Bacterial microcompartment domain / CcmK-like superfamily / BMC / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Bacterial microcompartment protein trimer-2
Similarity search - Component
Biological speciesHaliangium ochraceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSutter, M. / Aussignargues, C. / Kerfeld, C.A.
CitationJournal: Science / Year: 2017
Title: Assembly principles and structure of a 6.5-MDa bacterial microcompartment shell.
Authors: Markus Sutter / Basil Greber / Clement Aussignargues / Cheryl A Kerfeld /
Abstract: Many bacteria contain primitive organelles composed entirely of protein. These bacterial microcompartments share a common architecture of an enzymatic core encapsulated in a selectively permeable ...Many bacteria contain primitive organelles composed entirely of protein. These bacterial microcompartments share a common architecture of an enzymatic core encapsulated in a selectively permeable protein shell; prominent examples include the carboxysome for CO fixation and catabolic microcompartments found in many pathogenic microbes. The shell sequesters enzymatic reactions from the cytosol, analogous to the lipid-based membrane of eukaryotic organelles. Despite available structural information for single building blocks, the principles of shell assembly have remained elusive. We present the crystal structure of an intact shell from , revealing the basic principles of bacterial microcompartment shell construction. Given the conservation among shell proteins of all bacterial microcompartments, these principles apply to functionally diverse organelles and can inform the design and engineering of shells with new functionalities.
History
DepositionMar 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
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
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: Microcompartments protein
B: Microcompartments protein
C: Microcompartments protein
D: Microcompartments protein
E: Microcompartments protein
F: Microcompartments protein


Theoretical massNumber of molelcules
Total (without water)137,4256
Polymers137,4256
Non-polymers00
Water11,800655
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19290 Å2
ΔGint-100 kcal/mol
Surface area37900 Å2
MethodPISA
2
A: Microcompartments protein
B: Microcompartments protein
C: Microcompartments protein


Theoretical massNumber of molelcules
Total (without water)68,7123
Polymers68,7123
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-28 kcal/mol
Surface area22790 Å2
MethodPISA
3
D: Microcompartments protein
E: Microcompartments protein
F: Microcompartments protein


Theoretical massNumber of molelcules
Total (without water)68,7123
Polymers68,7123
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5550 Å2
ΔGint-13 kcal/mol
Surface area22840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.117, 126.106, 139.841
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein
Microcompartments protein


Mass: 22904.137 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haliangium ochraceum (strain DSM 14365 / JCM 11303 / SMP-2) (bacteria)
Strain: DSM 14365 / JCM 11303 / SMP-2 / Gene: Hoch_5816 / Production host: Escherichia coli (E. coli) / References: UniProt: D0LID6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 655 / 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: 2.19 Å3/Da / Density % sol: 43.71 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Na Acetate pH 5.1 1.6 M MgSO4

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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: Feb 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976484 Å / Relative weight: 1
ReflectionResolution: 1.7→38.59 Å / Num. obs: 131926 / % possible obs: 99.4 % / Redundancy: 14.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.122 / Net I/σ(I): 21
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 14.8 % / Rmerge(I) obs: 1.613 / Num. unique obs: 18813 / CC1/2: 0.695 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX(dev_2650: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HT5

4ht5


Resolution: 1.7→38.587 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2656 2000 1.52 %random selection
Rwork0.2255 ---
obs0.2261 131797 99.23 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→38.587 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9058 0 0 655 9713
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039214
X-RAY DIFFRACTIONf_angle_d0.58712537
X-RAY DIFFRACTIONf_dihedral_angle_d13.6215559
X-RAY DIFFRACTIONf_chiral_restr0.0421479
X-RAY DIFFRACTIONf_plane_restr0.0031640
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7001-1.74270.33861380.32298937X-RAY DIFFRACTION97
1.7427-1.78980.3651410.30779137X-RAY DIFFRACTION99
1.7898-1.84240.39611400.2849155X-RAY DIFFRACTION99
1.8424-1.90190.3051410.26779137X-RAY DIFFRACTION99
1.9019-1.96990.3111420.25519181X-RAY DIFFRACTION99
1.9699-2.04870.2911420.25159188X-RAY DIFFRACTION99
2.0487-2.1420.31451420.24899241X-RAY DIFFRACTION99
2.142-2.25490.29041420.22889245X-RAY DIFFRACTION99
2.2549-2.39620.25731430.22929259X-RAY DIFFRACTION100
2.3962-2.58110.27991440.22059320X-RAY DIFFRACTION100
2.5811-2.84080.28171440.21459344X-RAY DIFFRACTION100
2.8408-3.25170.2471440.21119429X-RAY DIFFRACTION100
3.2517-4.09610.19981470.19289464X-RAY DIFFRACTION100
4.0961-38.59740.2381500.20979760X-RAY DIFFRACTION100

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