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- PDB-1qhl: CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF MUKB AT 2.2A RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1qhl
TitleCRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF MUKB AT 2.2A RESOLUTION
ComponentsPROTEIN (CELL DIVISION PROTEIN MUKB)
KeywordsCELL DIVISION PROTEIN / MUKB / SMC / CHROMOSOME PARTITIONING
Function / homology
Function and homology information


condensin complex / nucleoid / chromosome condensation / sister chromatid cohesion / chromosome segregation / DNA replication / cell division / GTP binding / DNA binding / ATP binding ...condensin complex / nucleoid / chromosome condensation / sister chromatid cohesion / chromosome segregation / DNA replication / cell division / GTP binding / DNA binding / ATP binding / identical protein binding / cytosol
Similarity search - Function
N-terminal domain of mukB / N-terminal domain of mukB - #10 / 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 / P-loop containing nucleoside triphosphate hydrolase ...N-terminal domain of mukB / N-terminal domain of mukB - #10 / 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 / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chromosome partition protein MukB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
Authorsvan den Ent, F. / Lowe, J.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: Crystal structure of the N-terminal domain of MukB: a protein involved in chromosome partitioning.
Authors: van den Ent, F. / Lockhart, A. / Kendrick-Jones, J. / Lowe, J.
History
DepositionMay 17, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Nov 10, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (CELL DIVISION PROTEIN MUKB)


Theoretical massNumber of molelcules
Total (without water)25,2471
Polymers25,2471
Non-polymers00
Water1,35175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.400, 111.400, 65.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622

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Components

#1: Protein PROTEIN (CELL DIVISION PROTEIN MUKB)


Mass: 25246.979 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Details: THIS PROTEIN IS LINKED TO A SYNTHETIC C-TERMINAL HIS TAG (GSHHHHHH). THE TAG WAS NOT SEEN IN THE ELECTRON DENSITY.
Source: (gene. exp.) Escherichia coli (E. coli) / Cellular location: CYTOSOL / Plasmid: PHIS17 / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: P22523
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.22 Å3/Da / Density % sol: 45 %
Crystal growpH: 4.9
Details: 0.1M NA-CITRATE PH 4.9, 18-22% PEG 600, 50MG/ML, DROPS 1+1
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 Msodium citrate1reservoir
218-22 %PEG6001reservoir
350 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 0.91, 0.9790, 0.9797, 1.2
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 1, 1999
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911
20.9791
30.97971
41.21
ReflectionResolution: 2.2→40 Å / Num. obs: 382097 / % possible obs: 99.6 % / Redundancy: 13.1 % / Biso Wilson estimate: 30.9 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 5
Reflection shellResolution: 2.2→2.34 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 2.9 / % possible all: 97.3

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Processing

Software
NameVersionClassification
CCP4model building
X-PLOR3.8refinement
MOSFLMV. 6.0data reduction
CCP4(SCALA)data scaling
CCP4phasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→10 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.292 563 5 %RANDOM
Rwork0.217 ---
obs-12023 99.6 %-
Displacement parametersBiso mean: 30.4 Å2
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1598 0 0 75 1673
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.49
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.61
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.62.5
X-RAY DIFFRACTIONx_mcangle_it03
X-RAY DIFFRACTIONx_scbond_it03
X-RAY DIFFRACTIONx_scangle_it03.5
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 10 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.217
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 30.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.61
X-RAY DIFFRACTIONx_mcbond_it2.62.5
X-RAY DIFFRACTIONx_scbond_it03
X-RAY DIFFRACTIONx_mcangle_it03
X-RAY DIFFRACTIONx_scangle_it03.5

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