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- PDB-7v8p: Crystal Structure of the MukE dimer -

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Basic information

Entry
Database: PDB / ID: 7v8p
TitleCrystal Structure of the MukE dimer
ComponentsChromosome partition protein MukE
KeywordsNUCLEAR PROTEIN / Structural maintenance of chromosomes / Chromatin remodeling
Function / homologyArc Repressor Mutant, subunit A - #2250 / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha / :
Function and homology information
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsQian, J.W. / Guo, L.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Crystal structure of the chromosome partition protein MukE homodimer.
Authors: Qian, J.W. / Wang, X.Y. / Deng, K. / Li, D.F. / Guo, L.
History
DepositionAug 23, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 5, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chromosome partition protein MukE


Theoretical massNumber of molelcules
Total (without water)25,9891
Polymers25,9891
Non-polymers00
Water724
1
A: Chromosome partition protein MukE

A: Chromosome partition protein MukE


Theoretical massNumber of molelcules
Total (without water)51,9792
Polymers51,9792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area1500 Å2
ΔGint-8 kcal/mol
Surface area20210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.560, 64.360, 62.250
Angle α, β, γ (deg.)90.000, 116.650, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Chromosome partition protein MukE


Mass: 25989.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria)
Gene: mukE, CQA91_05990, DQP17_14640, NCTC8524_01712, NCTC9783_04161, SAMEA3710514_03893, SAMEA3710568_03348
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A383JZS2
#2: Water ChemComp-HOH / 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: 2.26 Å3/Da / Density % sol: 45.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 0.2 M Sodium chloride;0.1 M IBS pH 8.5;25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 11, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.439→55.64 Å / Num. obs: 8635 / % possible obs: 99.3 % / Redundancy: 7.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.037 / Rrim(I) all: 0.101 / Net I/σ(I): 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.44-2.547.20.92469329580.8790.3660.9952.298.6
8.79-55.646.20.05112421990.9960.0210.05529.698.9

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EUH

3euh


Resolution: 2.44→32.656 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 33.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2628 411 4.78 %
Rwork0.2199 8193 -
obs0.222 8604 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 133.8 Å2 / Biso mean: 68.365 Å2 / Biso min: 30.14 Å2
Refinement stepCycle: final / Resolution: 2.44→32.656 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1598 0 0 4 1602
Biso mean---59.53 -
Num. residues----195
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.44-2.79180.3311320.2729268998
2.7918-3.51670.33051220.2521274099
3.5167-32.6560.23071570.1967276499
Refinement TLS params.Method: refined / Origin x: -0.8302 Å / Origin y: 34.4444 Å / Origin z: -16.9704 Å
111213212223313233
T0.3214 Å2-0.0105 Å2-0.0462 Å2-0.4546 Å20.001 Å2--0.4119 Å2
L2.4977 °20.3621 °2-1.2066 °2-2.2355 °2-0.4837 °2--6.3631 °2
S-0.0227 Å °0.2748 Å °0.2652 Å °-0.0953 Å °0.2039 Å °0.152 Å °0.4819 Å °-0.6946 Å °-0.1597 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 1 through 220)

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