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- PDB-4ei7: Crystal structure of Bacillus cereus TubZ, GDP-form -

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Basic information

Entry
Database: PDB / ID: 4ei7
TitleCrystal structure of Bacillus cereus TubZ, GDP-form
ComponentsPlasmid replication protein RepX
KeywordsREPLICATION / GTP Hydrolase / plasmid segregation
Function / homology
Function and homology information


plasmid partitioning / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
60s Ribosomal Protein L30; Chain: A; - #190 / : / Tubulin-like protein TubZ, C-terminal domain / Tubulin-like protein FtsZ/CetZ / Tubulin/FtsZ, GTPase domain / 60s Ribosomal Protein L30; Chain: A; / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily ...60s Ribosomal Protein L30; Chain: A; - #190 / : / Tubulin-like protein TubZ, C-terminal domain / Tubulin-like protein FtsZ/CetZ / Tubulin/FtsZ, GTPase domain / 60s Ribosomal Protein L30; Chain: A; / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Tubulin-like protein TubZ
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsHayashi, I. / Hoshino, S.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Filament formation of the FtsZ/tubulin-like protein TubZ from the Bacillus cereus pXO1 plasmid.
Authors: Hoshino, S. / Hayashi, I.
History
DepositionApr 5, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Plasmid replication protein RepX
B: Plasmid replication protein RepX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,1314
Polymers87,2442
Non-polymers8862
Water6,612367
1
A: Plasmid replication protein RepX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0652
Polymers43,6221
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Plasmid replication protein RepX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0652
Polymers43,6221
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.826, 76.015, 96.931
Angle α, β, γ (deg.)90.000, 104.590, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Plasmid replication protein RepX


Mass: 43622.066 Da / Num. of mol.: 2 / Fragment: C-terminus truncation, UNP RESIDUES 1-389
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 10987 / Gene: repX, BCE_A0070 / Plasmid: pET23d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q74P24
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 367 / 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 Å3/Da / Density % sol: 38.35 % / Mosaicity: 0.555 °
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.5
Details: 50% PEG 400, 0.1M MES, 1mM GTPgammaS, pH 5.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 28, 2011 / Details: mirror
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 52862 / % possible obs: 97.8 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.059 / Χ2: 0.84 / Net I/σ(I): 11.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.9350.46425760.971196.9
1.93-1.9750.39526100.928197
1.97-2.0150.32626070.896196.8
2.01-2.055.10.28126510.865197.2
2.05-2.095.10.25725700.983197.2
2.09-2.145.20.2126410.86197.5
2.14-2.195.20.17126100.869197.4
2.19-2.255.30.16226581.064197.6
2.25-2.325.20.14326540.883198
2.32-2.395.20.11825840.847197.9
2.39-2.485.30.10326680.817197.9
2.48-2.585.30.0926700.822198.3
2.58-2.75.30.07426420.794198.1
2.7-2.845.30.06626370.801198.4
2.84-3.025.30.05426880.808198.4
3.02-3.255.20.04826500.924198.5
3.25-3.585.20.03826770.877198.7
3.58-4.095.30.0326970.684198.7
4.09-5.165.30.02526830.563198.6
5.16-505.10.02726890.588196.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.237 5191 9.6 %
Rwork0.1849 --
obs-51103 94.4 %
Solvent computationBsol: 53.7148 Å2
Displacement parametersBiso max: 73.12 Å2 / Biso mean: 27.1697 Å2 / Biso min: 6.96 Å2
Baniso -1Baniso -2Baniso -3
1-4.011 Å20 Å20.351 Å2
2---0.374 Å20 Å2
3----3.637 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6030 0 56 367 6453
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it3.031.5
X-RAY DIFFRACTIONc_scbond_it4.8872
X-RAY DIFFRACTIONc_mcangle_it3.7242
X-RAY DIFFRACTIONc_scangle_it6.5722.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ion.param
X-RAY DIFFRACTION5carbohydrate.param
X-RAY DIFFRACTION6gdp3.param

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