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- PDB-2xj4: Structure of the bacterial cell division regulator protein MipZ -

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Basic information

Entry
Database: PDB / ID: 2xj4
TitleStructure of the bacterial cell division regulator protein MipZ
ComponentsMIPZ
KeywordsREPLICATION / CELL DIVISION / ATPASE / WACA
Function / homology
Function and homology information


ATPase MipZ / ATPase MipZ / : / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Division plane positioning ATPase MipZ / Division plane positioning ATPase MipZ
Similarity search - Component
Biological speciesCAULOBACTER CRESCENTUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsMichie, K.A. / Lowe, J.
CitationJournal: Mol.Cell / Year: 2012
Title: Localized Dimerization and Nucleoid Binding Drive Gradient Formation by the Bacterial Cell Division Inhibitor Mipz.
Authors: Kiekebusch, D. / Michie, K.A. / Essen, L.O. / Lowe, J. / Thanbichler, M.
History
DepositionJul 2, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Database references / Other / Version format compliance
Revision 1.2May 30, 2012Group: Other
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MIPZ


Theoretical massNumber of molelcules
Total (without water)31,7631
Polymers31,7631
Non-polymers00
Water6,359353
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.334, 81.334, 124.206
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-2028-

HOH

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Components

#1: Protein MIPZ / DIVISION PLANE POSITIONING ATPASE MIPZ


Mass: 31763.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CAULOBACTER CRESCENTUS (bacteria) / Strain: CB15N / Description: PCR OF GENOMIC DNA SUPPLIED BY ATCC (19089D) / Plasmid: PHIS17 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): AI / References: UniProt: B8GY04, UniProt: A0A0H3CA70*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / 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: 2.5 Å3/Da / Density % sol: 50.7 % / Description: NONE
Crystal growpH: 6.5 / Details: 0.1 M MES/NAOH PH6.5, 30% V/V PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9747
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 16, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9747 Å / Relative weight: 1
ReflectionResolution: 1.5→20.69 Å / Num. obs: 40200 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 18.813 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.6
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 5.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
SCALAdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.6→61.31 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.612 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.17531 1993 4.9 %RANDOM
Rwork0.12621 ---
obs0.12863 38271 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.685 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å2-0.18 Å20 Å2
2---0.35 Å20 Å2
3---0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.6→61.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2104 0 0 353 2457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0222145
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4741.9732905
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3065271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.15922.42499
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.79215374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.0811527
X-RAY DIFFRACTIONr_chiral_restr0.2330.2333
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021623
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2540.21061
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3250.21518
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2490.2277
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.238
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3680.230
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1581.51388
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.24422159
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.2343849
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.6354.5745
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr3.83132237
X-RAY DIFFRACTIONr_sphericity_free13.6313353
X-RAY DIFFRACTIONr_sphericity_bonded8.58932109
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.207 146 -
Rwork0.108 2818 -
obs--99.4 %

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