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- PDB-3ku7: Crystal structure of Helicobacter pylori MinE, a cell division to... -

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Basic information

Entry
Database: PDB / ID: 3ku7
TitleCrystal structure of Helicobacter pylori MinE, a cell division topological specificity factor
ComponentsCell division topological specificity factor
KeywordsCELL CYCLE / Helicobacter pylori / MinE / Cell division
Function / homology
Function and homology information


regulation of division septum assembly / cell cycle / cell division
Similarity search - Function
Cell division topological specificity factor MinE / Cell Cycle; Chain A / Cell division topological specificity factor MinE superfamily / Septum formation topological specificity factor MinE / Cell division topological specificity factor MinE / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Cell division topological specificity factor
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsKang, G.B. / Song, H.E. / Kim, M.K. / Eom, S.H.
CitationJournal: Mol.Microbiol. / Year: 2010
Title: Crystal structure of Helicobacter pylori MinE, a cell division topological specificity factor
Authors: Kang, G.B. / Song, H.E. / Kim, M.K. / Youn, H.S. / Lee, J.G. / An, J.Y. / Chun, J.S. / Jeon, H. / Eom, S.H.
History
DepositionNov 26, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 12, 2014Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell division topological specificity factor
B: Cell division topological specificity factor


Theoretical massNumber of molelcules
Total (without water)18,4312
Polymers18,4312
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-18 kcal/mol
Surface area7280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.840, 70.840, 65.509
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

#1: Protein Cell division topological specificity factor / MinE


Mass: 9215.669 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: minE / Production host: Escherichia coli (E. coli) / References: UniProt: O25099

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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: 2.57 Å3/Da / Density % sol: 52.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM MES-NaOH (pH 6.5), 26% (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPAL/PLS 4A11
SYNCHROTRONPhoton Factory BL-5A20.97964, 0.97912, 0.98325, 0.96440
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDOct 17, 2007
ADSC QUANTUM 3152CCD
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1DOUBLE CRYSTAL MONOCHROMATORSINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.979641
30.979121
40.983251
50.96441
ReflectionResolution: 2.8→50 Å / Num. all: 4582 / Num. obs: 4582 / % possible obs: 99.7 %
Reflection shellResolution: 2.8→2.85 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
CNS1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.8→44.78 Å / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.298 510 10.9 %random
Rwork0.268 ---
all0.282 4680 --
obs0.268 4582 --
Solvent computationBsol: 45.058 Å2
Displacement parametersBiso mean: 64.661 Å2
Baniso -1Baniso -2Baniso -3
1--6.751 Å2-19.819 Å20 Å2
2---6.751 Å20 Å2
3---13.502 Å2
Refinement stepCycle: LAST / Resolution: 2.8→44.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms972 0 0 0 972
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.8
LS refinement shellResolution: 2.8→2.98 Å /
RfactorNum. reflection
Rfree0.354 -
Rwork0.352 -
obs-682

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