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- PDB-3euk: Crystal structure of MukE-MukF(residues 292-443)-MukB(head domain... -

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Basic information

Entry
Database: PDB / ID: 3euk
TitleCrystal structure of MukE-MukF(residues 292-443)-MukB(head domain)-ATPgammaS complex, asymmetric dimer
Components
  • Chromosome partition protein mukB, Linker
  • Chromosome partition protein mukE
  • Chromosome partition protein mukF
KeywordsCELL CYCLE / MukB / MukE / MukF / Chromosome condensation / condensin / SMC / non-SMC subunit / ABC-type ATPase / WHD / ATP-binding / Cell division / Chromosome partition / DNA condensation / DNA-binding / Nucleotide-binding
Function / homology
Function and homology information


nucleoid / chromosome condensation / chromosome segregation / DNA replication / cell division / calcium ion binding / DNA binding / ATP binding / cytoplasm
Similarity search - Function
MukF, C-terminal domain / Arc Repressor Mutant, subunit A - #2250 / N-terminal domain of mukB / N-terminal domain of mukB - #10 / 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 ...MukF, C-terminal domain / Arc Repressor Mutant, subunit A - #2250 / N-terminal domain of mukB / N-terminal domain of mukB - #10 / 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 / MukB, N-terminal domain / Chromosome partition protein MukB / MukB, hinge domain / MukB, hinge domain superfamily / : / MukB N-terminal / MukB hinge domain / NK-Lysin / SbcC/RAD50-like, Walker B motif / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Chromosome partition protein MukF / Chromosome partition protein MukE / Chromosome partition protein MukB
Similarity search - Component
Biological speciesHaemophilus ducreyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 4 Å
AuthorsWoo, J.S. / Lim, J.H. / Shin, H.C. / 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 1.2Feb 15, 2012Group: Non-polymer description
Revision 1.3Jun 28, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.4Oct 25, 2017Group: Refinement description / Category: software
Revision 1.5Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chromosome partition protein mukB, Linker
C: Chromosome partition protein mukB, Linker
E: Chromosome partition protein mukF
F: Chromosome partition protein mukB, Linker
H: Chromosome partition protein mukB, Linker
J: Chromosome partition protein mukF
L: Chromosome partition protein mukE
M: Chromosome partition protein mukE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)306,90116
Polymers304,7118
Non-polymers2,1908
Water00
1
A: Chromosome partition protein mukB, Linker
C: Chromosome partition protein mukB, Linker
E: Chromosome partition protein mukF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,6357
Polymers125,5403
Non-polymers1,0954
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9320 Å2
ΔGint-58 kcal/mol
Surface area47070 Å2
MethodPISA
2
F: Chromosome partition protein mukB, Linker
H: Chromosome partition protein mukB, Linker
J: Chromosome partition protein mukF
L: Chromosome partition protein mukE
M: Chromosome partition protein mukE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,2669
Polymers179,1715
Non-polymers1,0954
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16260 Å2
ΔGint-82 kcal/mol
Surface area61580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.414, 172.414, 491.587
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

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


Mass: 54102.809 Da / Num. of mol.: 4 / Fragment: Head domain / Mutation: E1435Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus ducreyi (strain 35000HP / ATCC 700724) (bacteria)
Gene: mukB, HD_1582 / Plasmid: pPROEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7VL96
#2: Protein Chromosome partition protein mukF


Mass: 17334.508 Da / Num. of mol.: 2 / Fragment: residues 292-443
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus ducreyi (bacteria) / Gene: mukF, HD_1585 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7VL94
#3: Protein Chromosome partition protein mukE


Mass: 26815.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus ducreyi (bacteria) / Gene: mukE, HD_1584 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7VL95
#4: Chemical
ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
Sequence detailsTHESE RESIDUES ARE NATURAL GENETIC VARIANTS, POLYMORPHISMS.

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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: 3.46 Å3/Da / Density % sol: 64.46 % / Mosaicity: 0.412 °
Crystal growTemperature: 296 K / Method: hanging drop / pH: 8
Details: PEG 10000, MgCl2, pH 8.0, hanging drop, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 9, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4→30 Å / Num. obs: 34959 / % possible obs: 92.8 % / Redundancy: 6 % / Rmerge(I) obs: 0.077 / Χ2: 0.84 / Net I/σ(I): 11.576
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
4-4.1430.22226060.518171.3
4.14-4.313.60.20829600.54180.1
4.31-4.54.70.20734820.563195.2
4.5-4.744.90.1835110.546194.7
4.74-5.045.80.16135890.596196.6
5.04-5.4260.15636470.601197.1
5.42-5.966.20.15136410.616197.2
5.96-6.826.70.12936890.767197.5
6.82-8.567.90.07937841.091198
8.56-308.90.03940501.441198.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.006data extraction
RefinementResolution: 4→20 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.756 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.324 1718 4.6 %
Rwork0.271 --
obs-34582 93.1 %
Solvent computationBsol: 35.472 Å2
Displacement parametersBiso max: 200 Å2 / Biso mean: 130.265 Å2 / Biso min: 26.49 Å2
Baniso -1Baniso -2Baniso -3
1-12.179 Å20 Å20 Å2
2--12.179 Å20 Å2
3----24.358 Å2
Refinement stepCycle: LAST / Resolution: 4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18273 0 128 0 18401
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.781.5
X-RAY DIFFRACTIONc_scbond_it1.8942
X-RAY DIFFRACTIONc_mcangle_it3.1462
X-RAY DIFFRACTIONc_scangle_it3.0822.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4ATG.param

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