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- PDB-3io0: Crystal structure of EtuB from Clostridium kluyveri -

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Basic information

Entry
Database: PDB / ID: 3io0
TitleCrystal structure of EtuB from Clostridium kluyveri
ComponentsEtuB protein
KeywordsSTRUCTURAL PROTEIN / Tamdem repeat of bacterial microcompartment domain in a single polypeptide chain
Function / homology
Function and homology information


bacterial microcompartment / structural molecule activity
Similarity search - Function
Bacterial microcompartment shell protein PduB / Bacterial microcompartment (BMC) circularly permuted domain / Bacterial microcompartment (BMC) circularly permuted domain profile. / BMC domain / Bacterial microcompartment domain / BMC / CcmK-like superfamily
Similarity search - Domain/homology
Predicted microcompartment protein
Similarity search - Component
Biological speciesClostridium kluyveri DSM 555 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3 Å
AuthorsPickersgill, R.W. / Warren, M.J.
CitationJournal: Biochem.J. / Year: 2009
Title: Structure of a trimeric bacterial microcompartment shell protein, EtuB, associated with ethanol utilisation in Clostridium kluyveri.
Authors: Heldt, D. / Frank, S. / Seyedarabi, A. / Ladakis, D. / Parsons, J.B. / Warren, M.J. / Pickersgill, R.W.
History
DepositionAug 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EtuB protein


Theoretical massNumber of molelcules
Total (without water)23,7561
Polymers23,7561
Non-polymers00
Water181
1
A: EtuB protein

A: EtuB protein

A: EtuB protein


Theoretical massNumber of molelcules
Total (without water)71,2693
Polymers71,2693
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area7850 Å2
ΔGint-57 kcal/mol
Surface area22320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.410, 173.410, 173.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

#1: Protein EtuB protein / Predicted microcompartment protein


Mass: 23756.201 Da / Num. of mol.: 1 / Fragment: UNP residues 75-304
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium kluyveri DSM 555 (bacteria)
Strain: ATCC8527, DSM555, NCIMB 10680 / Gene: 1073 / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) plysS / References: UniProt: A5N734
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 9.14 Å3/Da / Density % sol: 86.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 4M formate in water, 8mg/ml protein, equal volumes of reservoir and protein formed the drop, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 27, 2008 / Details: Si (111)
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 3→86.7 Å / Num. all: 17475 / Num. obs: 17475 / % possible obs: 100 % / Observed criterion σ(F): 187378 / Observed criterion σ(I): 187378 / Redundancy: 10.7 % / Biso Wilson estimate: 68.3 Å2 / Rmerge(I) obs: 0.151 / Net I/σ(I): 16.8
Reflection shellResolution: 3→3.17 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 3.3 / Num. unique all: 2522 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MIR / Resolution: 3→86.71 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.926 / SU B: 7.877 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20337 883 5.1 %RANDOM
Rwork0.188 ---
obs0.18877 17475 100 %-
all-17475 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.849 Å2
Refinement stepCycle: LAST / Resolution: 3→86.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1657 0 0 1 1658
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221680
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8231.9692277
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.1125228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.93924.38657
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.23615278
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.852158
X-RAY DIFFRACTIONr_chiral_restr0.1340.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021224
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2450.2864
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.21180
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.254
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.252
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4251.51143
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.78821799
X-RAY DIFFRACTIONr_scbond_it1.1173577
X-RAY DIFFRACTIONr_scangle_it1.9794.5478
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.003→3.081 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 71 -
Rwork0.306 1216 -
obs--100 %

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