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

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Basic information

Entry
Database: PDB / ID: 3euj
TitleCrystal structure of MukE-MukF(residues 292-443)-MukB(head domain)-ATPgammaS complex, symmetric dimer
Components
  • Chromosome partition protein mukB, Linker
  • 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 / N-terminal domain of mukB / N-terminal domain of mukB - #10 / 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, C-terminal domain / N-terminal domain of mukB / N-terminal domain of mukB - #10 / 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 / 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 MukB
Similarity search - Component
Biological speciesHaemophilus ducreyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.1 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

Downloads & links

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Assembly

Deposited unit
A: Chromosome partition protein mukB, Linker
B: Chromosome partition protein mukF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9854
Polymers71,4372
Non-polymers5482
Water54030
1
A: Chromosome partition protein mukB, Linker
B: Chromosome partition protein mukF
hetero molecules

A: Chromosome partition protein mukB, Linker
B: Chromosome partition protein mukF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,9708
Polymers142,8754
Non-polymers1,0954
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area11120 Å2
ΔGint-58 kcal/mol
Surface area45500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.522, 180.203, 138.496
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221

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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.: 1 / 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.: 1 / 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: 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.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
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: 2

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Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.13 %
Description: The crystal contains MukE molecules, but the model of MukE was not built in this structure because the protein exhibited only blobs of electron densities.
Mosaicity: 0.662 °
Crystal growTemperature: 296 K / Method: hanging drop / pH: 7 / Details: Succinate, pH 7.0, hanging drop, temperature 296K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPAL/PLS 4A11
SYNCHROTRONPAL/PLS 4A21.0064
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDNov 2, 2007
ADSC QUANTUM 2102CCDNov 2, 2007
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.00641
ReflectionRedundancy: 7.2 % / Av σ(I) over netI: 20.75 / Number: 175609 / Rmerge(I) obs: 0.129 / Χ2: 3.68 / D res high: 3.17 Å / D res low: 50 Å / Num. obs: 24252 / % possible obs: 91.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.82509910.0787.94810.7
5.426.8299.110.1333.6749.2
4.735.4298.310.1232.9859.4
4.34.7398.210.1412.6388.9
3.994.395.710.162.1447.2
3.763.9995.710.2262.0346.4
3.573.769810.2752.4688.2
3.413.5788.810.3082.1543.8
3.283.418110.3693.2762.9
3.173.2859.810.3953.0282.2
ReflectionResolution: 3.1→30 Å / Num. obs: 24721 / % possible obs: 90.2 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.066 / Χ2: 1.391 / Net I/σ(I): 20.751
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.1-3.212.80.16319700.9281,273.3
3.21-3.343.40.15521670.9941,280.4
3.34-3.494.10.14523291.1171,286.5
3.49-3.6750.1224691.1631,291.3
3.67-3.960.10324961.2441,292.2
3.9-4.217.10.08125101.4151,292.3
4.21-4.638.50.07525601.5241,294.7
4.63-5.299.20.06626411.5041,295.6
5.29-6.668.90.06626961.431,296.9
6.66-309.60.04328831.5371,297.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: SAD / Resolution: 3.1→30 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.806 / σ(F): 0
Details: the mattews coeffincient and solvent content have been calculated with the total molecular weight of all molecules in the asymmetric unit of the crystal, including two MukE molecules and all ...Details: the mattews coeffincient and solvent content have been calculated with the total molecular weight of all molecules in the asymmetric unit of the crystal, including two MukE molecules and all missing residues of MukF and MukB.
RfactorNum. reflection% reflection
Rfree0.291 1204 4.4 %
Rwork0.259 --
obs-24409 89 %
Solvent computationBsol: 10 Å2
Displacement parametersBiso max: 133.31 Å2 / Biso mean: 53.833 Å2 / Biso min: 1 Å2
Baniso -1Baniso -2Baniso -3
1-20.068 Å20 Å20 Å2
2---35.047 Å20 Å2
3---14.979 Å2
Refinement stepCycle: LAST / Resolution: 3.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4162 0 32 30 4224
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.5611.5
X-RAY DIFFRACTIONc_scbond_it1.7792
X-RAY DIFFRACTIONc_mcangle_it2.8192
X-RAY DIFFRACTIONc_scangle_it2.9862.5
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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