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- PDB-2xj9: Dimer Structure of the bacterial cell division regulator MipZ -

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Basic information

Entry
Database: PDB / ID: 2xj9
TitleDimer Structure of the bacterial cell division regulator MipZ
ComponentsMIPZ
KeywordsREPLICATION / CELL DIVISION / ATPASE / WACA
Function / homology
Function and homology information


ATPase MipZ / ATPase MipZ / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Division plane positioning ATPase MipZ / MipZ
Similarity search - Component
Biological speciesCAULOBACTER CRESCENTUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 ...Database references / Other / Refinement description / Version format compliance
Revision 1.2May 30, 2012Group: Other
Revision 1.3Jan 30, 2013Group: Atomic model / Derived calculations / Non-polymer description
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MIPZ
B: MIPZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5346
Polymers63,4392
Non-polymers1,0954
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-31.8 kcal/mol
Surface area21380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.122, 57.122, 164.856
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 4:147 OR RESSEQ 155:174 OR RESSEQ...
211CHAIN B AND (RESSEQ 4:147 OR RESSEQ 155:174 OR RESSEQ...

NCS oper: (Code: given / Matrix: (1), (1), (1))

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Components

#1: Protein MIPZ / DIVISION PLANE POSITIONING ATPASE MIPZ


Mass: 31719.348 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CAULOBACTER CRESCENTUS (bacteria) / Strain: CB15N
Description: PCRED FROM GENOMIC DNA FROM ATCC 19089D. MUTATION CONSTRUCTED BY SPLICE-OVERLAP EXTENSION.
Plasmid: PHIS17 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): AI / References: UniProt: B8GY04, UniProt: Q9A6C9*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.1 Å3/Da / Density % sol: 42.1 % / Description: NONE
Crystal growpH: 8.5 / Details: 20 MM TRIS PH 8.5, 23.6% ETHANOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8726
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 16, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.8→39.2 Å / Num. obs: 10750 / % possible obs: 94.2 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 48.51 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.9
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.7 / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XJ4
Resolution: 2.8→28.847 Å / SU ML: 0.45 / σ(F): 1.12 / Phase error: 27.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2399 1117 5.1 %
Rwork0.1851 --
obs0.1881 21906 85.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.315 Å2 / ksol: 0.276 e/Å3
Displacement parametersBiso mean: 49.339 Å2
Baniso -1Baniso -2Baniso -3
1-6.3893 Å20 Å20 Å2
2--6.3893 Å20 Å2
3----12.7787 Å2
Refinement stepCycle: LAST / Resolution: 2.8→28.847 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4123 0 64 54 4241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014255
X-RAY DIFFRACTIONf_angle_d1.535768
X-RAY DIFFRACTIONf_dihedral_angle_d19.0541599
X-RAY DIFFRACTIONf_chiral_restr0.075658
X-RAY DIFFRACTIONf_plane_restr0.006741
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1886X-RAY DIFFRACTIONPOSITIONAL
12B1886X-RAY DIFFRACTIONPOSITIONAL0.11
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8002-2.92750.37581450.29712613X-RAY DIFFRACTION86
2.9275-3.08170.30091350.23832640X-RAY DIFFRACTION86
3.0817-3.27460.30041240.21082620X-RAY DIFFRACTION86
3.2746-3.5270.27821430.19592615X-RAY DIFFRACTION86
3.527-3.88120.25481270.16862609X-RAY DIFFRACTION85
3.8812-4.4410.21431300.15522576X-RAY DIFFRACTION85
4.441-5.58850.18631370.14132586X-RAY DIFFRACTION85
5.5885-28.8490.17481760.14962530X-RAY DIFFRACTION84

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