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- PDB-7x3h: The structure of Clostridium botulinum ParM in the apo conformation -

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Basic information

Entry
Database: PDB / ID: 7x3h
TitleThe structure of Clostridium botulinum ParM in the apo conformation
ComponentsCBg-ParM triple mutant R204D, K230D and N234D
KeywordsSTRUCTURAL PROTEIN / ParM
Function / homologyATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Function and homology information
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsRobinson, R.C. / Ali, S. / Narita, A.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18H02410 Japan
Japan Society for the Promotion of Science (JSPS)21H02440 Japan
Japan Science and TechnologyJPMJCR19S5 Japan
CitationJournal: To Be Published
Title: Structure of tubulin H393D mutant from Odinarchaeota
Authors: Robinson, R.C. / Ali, S. / Narita, A.
History
DepositionMar 1, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CBg-ParM triple mutant R204D, K230D and N234D


Theoretical massNumber of molelcules
Total (without water)32,8901
Polymers32,8901
Non-polymers00
Water5,657314
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14060 Å2
Unit cell
Length a, b, c (Å)55.635, 51.103, 64.917
Angle α, β, γ (deg.)90.000, 115.280, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein CBg-ParM triple mutant R204D, K230D and N234D


Mass: 32890.355 Da / Num. of mol.: 1 / Mutation: R204D, K230D, N234D
Source method: isolated from a genetically manipulated source
Details: Depositor reference: GB ED787363.1 / Source: (gene. exp.) Clostridium botulinum (bacteria) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.54 Å3/Da / Density % sol: 51.52 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 5 mg/ml CBg-ParM mutant 1 mM AMPPNP 0.2 M ammonium chloride 22% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 35734 / % possible obs: 97.55 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.03 / Rpim(I) all: 0.018 / Net I/σ(I): 37.7
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2896 / CC1/2: 0.736 / Rpim(I) all: 0.343

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Processing

Software
NameVersionClassification
PHENIX1.17.1refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→32 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.224 --
Rwork0.192 --
obs-35734 99.3 %
Displacement parametersBiso mean: 26.42 Å2
Refinement stepCycle: LAST / Resolution: 1.7→32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2196 0 0 314 2510
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00592291
X-RAY DIFFRACTIONf_angle_d0.7163104
X-RAY DIFFRACTIONf_chiral_restr0.0496357
X-RAY DIFFRACTIONf_plane_restr0.0051396
X-RAY DIFFRACTIONf_dihedral_angle_d17.0735878
LS refinement shellResolution: 1.7→1.73 Å
RfactorNum. reflection% reflection
Rfree0.299 --
Rwork0.271 2896 -
obs--94.1 %

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