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- PDB-3euh: Crystal Structure of the MukE-MukF Complex -

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Basic information

Entry
Database: PDB / ID: 3euh
TitleCrystal Structure of the MukE-MukF Complex
Components
  • Chromosome partition protein mukF
  • MukE
KeywordsCELL CYCLE / Chromosome condensation / condensin / non-SMC subunit / kleisin / MukE / MukF / Calcium / Cell division / Chromosome partition / Cytoplasm / DNA condensation
Function / homology
Function and homology information


condensin complex / nucleoid / chromosome condensation / chromosome segregation / DNA replication / cell cycle / cell division / calcium ion binding / cytoplasm
Similarity search - Function
MukE-like family, C-terminal domain / Arc Repressor Mutant, subunit A - #2250 / Chromosome partition protein MukF, middle domain / Prokaryotic chromosome segregation/condensation protein MukE / MukE, C-terminal domain / MukE, N-terminal domain / MukE-like family / Chromosome partition protein MukF / Chromosome partition protein MukF, winged-helix domain / Chromosome partition protein MukF, middle domain ...MukE-like family, C-terminal domain / Arc Repressor Mutant, subunit A - #2250 / Chromosome partition protein MukF, middle domain / Prokaryotic chromosome segregation/condensation protein MukE / MukE, C-terminal domain / MukE, N-terminal domain / MukE-like family / Chromosome partition protein MukF / Chromosome partition protein MukF, winged-helix domain / Chromosome partition protein MukF, middle domain / Chromosome partition protein MukF, C-terminal domain / MukF, middle domain superfamily / MukF, C-terminal domain superfamily / MukF winged-helix domain / MukF middle domain / MukF C-terminal domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
GLYCINE / Chromosome partition protein MukE / Chromosome partition protein MukF / Chromosome partition protein MukE
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.9 Å
AuthorsSuh, M.K. / Ku, B. / Ha, N.C. / Woo, J.S. / Oh, B.H.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2009
Title: Structural studies of a bacterial condensin complex reveal ATP-dependent disruption of intersubunit interactions.
Authors: Woo, J.S. / Lim, J.H. / Shin, H.C. / Suh, M.K. / Ku, B. / Lee, K.H. / Joo, K. / Robinson, H. / Lee, J. / Park, S.Y. / Ha, N.C. / Oh, B.H.
History
DepositionOct 10, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chromosome partition protein mukF
B: Chromosome partition protein mukF
C: MukE
D: MukE
E: MukE
F: MukE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,59810
Polymers209,2976
Non-polymers3004
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22410 Å2
ΔGint-135 kcal/mol
Surface area66700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.338, 151.146, 188.072
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Chromosome partition protein mukF / Protein kicB


Mass: 50635.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P60293
#2: Protein
MukE


Mass: 27006.484 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6ITT5, UniProt: P22524*PLUS
#3: Chemical
ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.16 % / Mosaicity: 0.497 °
Crystal growTemperature: 287 K / Method: vapor diffusion / pH: 6.5
Details: PEG 400, CaCl2, MgAcet, glycine, pH 6.5, vapor diffusion, temperature 287K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory AR-NW12A11
SYNCHROTRONNSLS X29A21.0039
SYNCHROTRONPAL/PLS 6B30.97903
Detector
IDDetectorDate
1CCDNov 12, 2005
2CCDJun 14, 2005
3CCDMay 21, 2005
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
3SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.00391
30.979031
ReflectionRedundancy: 4.9 % / Av σ(I) over netI: 31.82 / Number: 196180 / Rmerge(I) obs: 0.09 / Χ2: 1.67 / D res high: 3.1 Å / D res low: 30 Å / Num. obs: 39887 / % possible obs: 97.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.663099.410.0582.4885.9
5.296.6698.710.092.0745.5
4.635.299910.092.0525.6
4.214.6398.610.0941.885.5
3.94.2197.610.1071.6885.3
3.673.997.210.1291.4344.8
3.493.6796.710.1461.254.6
3.343.4995.910.1691.0844.2
3.213.3495.510.1880.783.9
3.13.2193.710.2180.6763.6
ReflectionResolution: 2.7→30 Å / Num. obs: 59926 / % possible obs: 97.1 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.065 / Χ2: 1.675 / Net I/σ(I): 31.821
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.7-2.83.80.22756090.49592.6
2.8-2.914.30.19857600.5594.8
2.91-3.044.90.1658550.6995.9
3.04-3.25.40.13259210.88297.1
3.2-3.46.10.10860141.19298.1
3.4-3.666.40.09259681.62297.5
3.66-4.0370.07960261.96597.9
4.03-4.617.60.06661742.30699.2
4.61-5.87.70.05962002.37599.5
5.8-307.30.04863992.50298.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.006data extraction
MLPHAREphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.9→20 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.834 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.274 2455 5 %
Rwork0.225 --
obs-48571 98 %
Solvent computationBsol: 19.531 Å2
Displacement parametersBiso max: 156.17 Å2 / Biso mean: 68.18 Å2 / Biso min: 16.69 Å2
Baniso -1Baniso -2Baniso -3
1--7.66 Å20 Å20 Å2
2---1.325 Å20 Å2
3---8.985 Å2
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11487 0 20 57 11564
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.5531.5
X-RAY DIFFRACTIONc_scbond_it1.9942
X-RAY DIFFRACTIONc_mcangle_it2.7232
X-RAY DIFFRACTIONc_scangle_it3.2632.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water.param
X-RAY DIFFRACTION3ion.param

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