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- PDB-6h2x: MukB coiled-coil elbow from E. coli -

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Basic information

Entry
Database: PDB / ID: 6h2x
TitleMukB coiled-coil elbow from E. coli
ComponentsChromosome partition protein MukB,Chromosome partition protein MukB
KeywordsDNA BINDING PROTEIN / chromosome organization / chromosome segregation / coiled coil
Function / homology
Function and homology information


condensin complex / nucleoid / chromosome condensation / sister chromatid cohesion / chromosome segregation / DNA replication / cell division / GTP binding / DNA binding / ATP binding ...condensin complex / nucleoid / chromosome condensation / sister chromatid cohesion / chromosome segregation / DNA replication / cell division / GTP binding / DNA binding / ATP binding / identical protein binding / cytosol
Similarity search - Function
MukB, N-terminal domain / Chromosome partition protein MukB / MukB, hinge domain / MukB, hinge domain superfamily / MukB N-terminal / MukB hinge domain / SbcC/RAD50-like, Walker B motif / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chromosome partition protein MukB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBuermann, F. / Lowe, J.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust202754/Z/16/Z United Kingdom
Medical Research Council (United Kingdom)U105184326 United Kingdom
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2019
Title: A folded conformation of MukBEF and cohesin.
Authors: Burmann, F. / Lee, B.G. / Than, T. / Sinn, L. / O'Reilly, F.J. / Yatskevich, S. / Rappsilber, J. / Hu, B. / Nasmyth, K. / Lowe, J.
History
DepositionJul 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 1, 2024Group: 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: Chromosome partition protein MukB,Chromosome partition protein MukB


Theoretical massNumber of molelcules
Total (without water)42,3571
Polymers42,3571
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area24310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.122, 35.036, 81.713
Angle α, β, γ (deg.)90.00, 93.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Chromosome partition protein MukB,Chromosome partition protein MukB / Structural maintenance of chromosome-related protein


Mass: 42356.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: mukB, b0924, JW0907 / Production host: Escherichia coli (E. coli) / References: UniProt: P22523
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.76 Å3/Da / Density % sol: 55.43 % / Description: Thin plates
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10 mM MES, 150 mM NaCl, 1 mM EDTA, 1 mM TCEP, 1 mM NaN3, 22% PEG3350, 0.25 M NaSCN

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 2.6→40.78 Å / Num. obs: 27424 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.041 / Net I/σ(I): 9.7
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.951 / Mean I/σ(I) obs: 2 / Num. unique obs: 1771 / CC1/2: 0.917 / Rpim(I) all: 0.39 / Rrim(I) all: 1.029 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
REFMAC(5.8.0189)refinement
Aimless(0.5.32)data scaling
XDS(Jun1-2017)data reduction
BUCCANEER(1.6.4)model building
Coot(0.8.8)model building
PHASER(2.8.0)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Initial model from SAD experiment

Resolution: 2.6→40.481 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 0.24 / Phase error: 38.81
RfactorNum. reflection% reflection
Rfree0.2968 1312 4.78 %
Rwork0.2434 --
obs0.2458 27424 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→40.481 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2844 0 0 4 2848
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022874
X-RAY DIFFRACTIONf_angle_d0.4253872
X-RAY DIFFRACTIONf_dihedral_angle_d20.4411809
X-RAY DIFFRACTIONf_chiral_restr0.027424
X-RAY DIFFRACTIONf_plane_restr0.002531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6001-2.70410.4391820.35642908X-RAY DIFFRACTION99
2.7041-2.82720.43241580.33232810X-RAY DIFFRACTION99
2.8272-2.97620.38071440.29552905X-RAY DIFFRACTION99
2.9762-3.16260.34741140.28932991X-RAY DIFFRACTION99
3.1626-3.40670.33871300.27652878X-RAY DIFFRACTION99
3.4067-3.74930.31741850.24822849X-RAY DIFFRACTION100
3.7493-4.29130.27351650.2272918X-RAY DIFFRACTION100
4.2913-5.40450.24391100.22682903X-RAY DIFFRACTION99
5.4045-40.4860.25071240.21092950X-RAY DIFFRACTION100

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