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- PDB-4mn4: Structural Basis for the MukB-topoisomerase IV Interaction -

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Basic information

Entry
Database: PDB / ID: 4mn4
TitleStructural Basis for the MukB-topoisomerase IV Interaction
Components
  • Chromosome partition protein MukB
  • DNA topoisomerase 4 subunit ATopoisomerase
KeywordsISOMERASE/CELL CYCLE / beta-pinwheel / chromosome partitioning / ISOMERASE-CELL CYCLE complex
Function / homology
Function and homology information


condensin complex / plasmid partitioning / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / nucleoid / chromosome condensation / sister chromatid cohesion / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / extrinsic component of plasma membrane / DNA topological change ...condensin complex / plasmid partitioning / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / nucleoid / chromosome condensation / sister chromatid cohesion / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / extrinsic component of plasma membrane / DNA topological change / chromosome segregation / chromosome / DNA replication / cell division / GTP binding / DNA binding / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
MukB, hinge domain / DNA topoisomerase IV, subunit A, Gram-negative / 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 / Immunoglobulin FC, subunit C ...MukB, hinge domain / DNA topoisomerase IV, subunit A, Gram-negative / 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 / Immunoglobulin FC, subunit C / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / DNA gyrase C-terminal domain, beta-propeller / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta / DNA gyrase/topoisomerase IV, subunit A / DNA Topoisomerase IV / DNA topoisomerase, type IIA-like domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Alpha-Beta Plaits / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA topoisomerase 4 subunit A / Chromosome partition protein MukB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD, MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsVos, S.M. / Stewart, N.K. / Oakley, M.G. / Berger, J.M.
CitationJournal: Embo J. / Year: 2013
Title: Structural basis for the MukB-topoisomerase IV interaction and its functional implications in vivo.
Authors: Vos, S.M. / Stewart, N.K. / Oakley, M.G. / Berger, J.M.
History
DepositionSep 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA topoisomerase 4 subunit A
C: Chromosome partition protein MukB
D: Chromosome partition protein MukB
B: DNA topoisomerase 4 subunit A


Theoretical massNumber of molelcules
Total (without water)93,2864
Polymers93,2864
Non-polymers00
Water4,522251
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.767, 103.737, 186.611
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA topoisomerase 4 subunit A / Topoisomerase / Topoisomerase IV subunit A


Mass: 28295.965 Da / Num. of mol.: 2 / Fragment: C-terminal domain (UNP residues 497-752)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 substr. MG1655 / Gene: parC / Plasmid: pET28(b) / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)Codon-Plus RIL / References: UniProt: P0AFI2, EC: 5.99.1.3
#2: Protein Chromosome partition protein MukB / Structural maintenance of chromosome-related protein


Mass: 18347.139 Da / Num. of mol.: 2 / Fragment: hinge domain (UNP residues 645-804)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 substr. MG1655 / Gene: mukB / Plasmid: pET28(b) / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)Codon-Plus RIL / References: UniProt: P22523
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.58 Å3/Da / Density % sol: 52.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 212.5 mM lithium citrate tribasic tetrahydrate, 20% PEG3350, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.3.111.1
SYNCHROTRONALS 8.3.120.979648
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDJun 24, 2010
ADSC QUANTUM 315r2CCDJun 24, 2010
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double flat crystal, Si(111)SINGLE WAVELENGTHMx-ray1
2Double flat crystal, Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
20.9796481
ReflectionResolution: 2.3→49.974 Å / Num. all: 44001 / Num. obs: 44001 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 17
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.395 / Num. unique all: 44001 / % possible all: 88.5

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD, MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3IBP AND IZVU

3ibp


Resolution: 2.3→49.974 Å / SU ML: 0.34 / σ(F): 0 / Phase error: 25.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2461 2170 5.04 %RANDOM
Rwork0.2042 ---
obs0.2063 43079 98.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→49.974 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6209 0 0 251 6460
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046421
X-RAY DIFFRACTIONf_angle_d0.6138720
X-RAY DIFFRACTIONf_dihedral_angle_d10.4482488
X-RAY DIFFRACTIONf_chiral_restr0.042982
X-RAY DIFFRACTIONf_plane_restr0.0031163
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.35010.31461310.25392220X-RAY DIFFRACTION87
2.3501-2.40480.3221510.27082307X-RAY DIFFRACTION92
2.4048-2.46490.36181370.27192461X-RAY DIFFRACTION96
2.4649-2.53150.33481390.24692578X-RAY DIFFRACTION100
2.5315-2.6060.28061290.24882587X-RAY DIFFRACTION100
2.606-2.69010.31041400.24822535X-RAY DIFFRACTION100
2.6901-2.78630.31821480.24552585X-RAY DIFFRACTION100
2.7863-2.89780.32861350.25172583X-RAY DIFFRACTION100
2.8978-3.02970.31721290.25262594X-RAY DIFFRACTION100
3.0297-3.18940.31531090.22942617X-RAY DIFFRACTION100
3.1894-3.38920.25011410.22072589X-RAY DIFFRACTION100
3.3892-3.65080.22461140.19712614X-RAY DIFFRACTION100
3.6508-4.0180.23311430.17962609X-RAY DIFFRACTION100
4.018-4.59910.18011480.15492635X-RAY DIFFRACTION99
4.5991-5.7930.18221230.162658X-RAY DIFFRACTION99
5.793-49.98580.17761530.17342737X-RAY DIFFRACTION97

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