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

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Basic information

Entry
Database: PDB / ID: 3mcd
TitleCrystal structure of Helicobacter pylori MinE, a cell division topological specificity factor
ComponentsCell division topological specificity factor
KeywordsCELL CYCLE / Cytokinesis / MinE / Topological specificity factor / 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: 3.2 Å
AuthorsKang, G.B. / Song, H.E. / Kim, M.K. / Youn, H.S. / Lee, J.G. / An, J.Y. / Jeon, H. / Chun, J.S. / 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
DepositionMar 29, 2010Deposition 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 19, 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

Downloads & links

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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
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-19 kcal/mol
Surface area6820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.458, 39.458, 155.405
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Cell division topological specificity factor


Mass: 9215.669 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: minE, HP_0332 / 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: 1

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Sample preparation

CrystalDensity Matthews: 1.89 Å3/Da / Density % sol: 35.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 100mM MES-NaOH (pH 6.5), 26% (w/v) PEG 3350, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.9796, 0.9791, 0.9833, 0.9644
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 28, 2007
RadiationMonochromator: CRYSTAL MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97961
20.97911
30.98331
40.96441
ReflectionResolution: 3→50 Å / Num. all: 4478 / Num. obs: 4478 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellHighest resolution: 3 Å / % possible all: 98.3

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Processing

Software
NameClassification
HKL-2000data collection
SOLVEphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 3.2→34.17 Å / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.303 464 10.4 %random
Rwork0.271 ---
all0.29 4478 --
obs0.29 4259 --
Solvent computationBsol: 300 Å2
Displacement parametersBiso mean: 74.847 Å2
Baniso -1Baniso -2Baniso -3
1--20.365 Å2-7.045 Å20 Å2
2---20.365 Å20 Å2
3---40.729 Å2
Refinement stepCycle: LAST / Resolution: 3.2→34.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms915 0 0 0 915
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.9
LS refinement shellResolution: 3.2→3.4 Å /
RfactorNum. reflection
Rwork0.322 -
Rfree-0
obs-608

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