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- PDB-6nlu: Circularly permuted Haliangium ochraceum BMC-H -

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Basic information

Entry
Database: PDB / ID: 6nlu
TitleCircularly permuted Haliangium ochraceum BMC-H
Componentscircularly permuted BMC-H
KeywordsSTRUCTURAL PROTEIN / bacterial microcompartment
Function / homology
Function and homology information


bacterial microcompartment
Similarity search - Function
Bacterial microcompartments protein, conserved site / Bacterial microcompartment (BMC) domain signature. / CcmK/CsoS1, bacterial microcompartment domain / : / Bacterial microcompartment (BMC) domain profile. / BMC domain / Bacterial microcompartment domain / BMC / CcmK-like superfamily
Similarity search - Domain/homology
Bacterial microcompartment protein homohexamer
Similarity search - Component
Biological speciesHaliangium ochraceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.607 Å
AuthorsSutter, M. / Ferlez, B. / Kerfeld, C.A.
CitationJournal: Metab. Eng. / Year: 2019
Title: A designed bacterial microcompartment shell with tunable composition and precision cargo loading.
Authors: Ferlez, B. / Sutter, M. / Kerfeld, C.A.
History
DepositionJan 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 11, 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: circularly permuted BMC-H
B: circularly permuted BMC-H


Theoretical massNumber of molelcules
Total (without water)21,1182
Polymers21,1182
Non-polymers00
Water2,414134
1
A: circularly permuted BMC-H
B: circularly permuted BMC-H

A: circularly permuted BMC-H
B: circularly permuted BMC-H

A: circularly permuted BMC-H
B: circularly permuted BMC-H


Theoretical massNumber of molelcules
Total (without water)63,3556
Polymers63,3556
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area11030 Å2
ΔGint-77 kcal/mol
Surface area23830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.492, 73.492, 119.590
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-259-

HOH

21B-240-

HOH

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Components

#1: Protein circularly permuted BMC-H


Mass: 10559.107 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haliangium ochraceum (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: D0LID5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.32 Å3/Da / Density % sol: 46.94 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.5 M Ammonium tartrate, 0.1 M sodium acetate pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.607→43.58 Å / Num. obs: 51230 / % possible obs: 99.9 % / Redundancy: 17.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.021 / Net I/σ(I): 18.6
Reflection shellResolution: 1.607→1.69 Å / Rmerge(I) obs: 0.448 / Num. unique obs: 7266 / CC1/2: 0.973 / Rpim(I) all: 0.109 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DJB

5djb


Resolution: 1.607→43.579 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2406 3663 7.82 %
Rwork0.209 --
obs0.2115 46864 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.607→43.579 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1404 0 0 134 1538
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011418
X-RAY DIFFRACTIONf_angle_d0.9871917
X-RAY DIFFRACTIONf_dihedral_angle_d3.502857
X-RAY DIFFRACTIONf_chiral_restr0.068228
X-RAY DIFFRACTIONf_plane_restr0.007253
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6066-1.62770.34281330.29061603X-RAY DIFFRACTION96
1.6277-1.650.32051430.27441667X-RAY DIFFRACTION100
1.65-1.67360.27631440.26031680X-RAY DIFFRACTION100
1.6736-1.69860.33531400.25761647X-RAY DIFFRACTION100
1.6986-1.72510.29541420.25571688X-RAY DIFFRACTION100
1.7251-1.75340.30461450.24511679X-RAY DIFFRACTION100
1.7534-1.78360.35291390.24511658X-RAY DIFFRACTION100
1.7836-1.8160.29061410.24281664X-RAY DIFFRACTION100
1.816-1.8510.2641410.22761668X-RAY DIFFRACTION100
1.851-1.88880.26171400.22291691X-RAY DIFFRACTION100
1.8888-1.92980.29061360.25591603X-RAY DIFFRACTION96
1.9298-1.97470.25961370.22281664X-RAY DIFFRACTION100
1.9747-2.02410.29871400.21081664X-RAY DIFFRACTION100
2.0241-2.07880.29561340.21781652X-RAY DIFFRACTION99
2.0788-2.140.21931450.20681674X-RAY DIFFRACTION100
2.14-2.20910.26281370.20671668X-RAY DIFFRACTION100
2.2091-2.2880.25751420.22251637X-RAY DIFFRACTION97
2.288-2.37960.21381460.19941665X-RAY DIFFRACTION100
2.3796-2.48790.22021430.19021647X-RAY DIFFRACTION100
2.4879-2.61910.24891400.19981678X-RAY DIFFRACTION100
2.6191-2.78310.27411430.19061675X-RAY DIFFRACTION100
2.7831-2.9980.18561430.19721663X-RAY DIFFRACTION100
2.998-3.29960.25251440.19431663X-RAY DIFFRACTION100
3.2996-3.77680.23181350.17821678X-RAY DIFFRACTION100
3.7768-4.75740.16121460.16671666X-RAY DIFFRACTION100
4.7574-43.59530.1911440.23441659X-RAY DIFFRACTION99

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