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- PDB-7c7y: C-terminal domain of B. cereus TubY -

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Basic information

Entry
Database: PDB / ID: 7c7y
TitleC-terminal domain of B. cereus TubY
ComponentsUncharacterized protein
KeywordsDNA BINDING PROTEIN / DNA segregation
Function / homologyDomain of unknown function DUF3967 / Protein of unknown function (DUF3967) / MerR HTH family regulatory protein / MerR-type HTH domain / regulation of DNA-templated transcription / DNA binding / MerR family transcriptional regulator
Function and homology information
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsHayashi, I.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: J.Biol.Chem. / Year: 2020
Title: The C-terminal region of the plasmid partitioning protein TubY is a tetramer that can bind membranes and DNA.
Authors: Hayashi, I.
History
DepositionMay 27, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed
Revision 1.2Mar 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.3Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)37,6924
Polymers37,6924
Non-polymers00
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11230 Å2
ΔGint-94 kcal/mol
Surface area15140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.053, 40.282, 80.669
Angle α, β, γ (deg.)101.97, 94.22, 98.52
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Uncharacterized protein


Mass: 9423.053 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (strain ATCC 10987 / NRS 248) (bacteria)
Strain: ATCC 10987 / NRS 248 / Gene: BCE_A0068 / Production host: Escherichia coli (E. coli) / References: UniProt: Q74P26
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.24 Å3/Da / Density % sol: 45.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.97911 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 9894 / % possible obs: 98 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 27.2
Reflection shellResolution: 2.6→2.64 Å / Rmerge(I) obs: 0.33 / Num. unique obs: 485

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
SCALEPACKdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→26.16 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.909 / SU B: 12.552 / SU ML: 0.257 / Cross valid method: THROUGHOUT / ESU R: 1.077 / ESU R Free: 0.356 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2772 466 4.7 %RANDOM
Rwork0.2243 ---
obs0.22674 9399 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.024 Å2
Baniso -1Baniso -2Baniso -3
1-6.02 Å20.85 Å2-3.65 Å2
2--2.3 Å2-2.84 Å2
3----5.76 Å2
Refinement stepCycle: 1 / Resolution: 2.6→26.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2165 0 0 17 2182
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132181
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172082
X-RAY DIFFRACTIONr_angle_refined_deg1.5191.672920
X-RAY DIFFRACTIONr_angle_other_deg1.3071.5864856
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9275259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.41224.203138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.62915434
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9571516
X-RAY DIFFRACTIONr_chiral_restr0.060.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022384
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02416
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.845.6911048
X-RAY DIFFRACTIONr_mcbond_other4.8395.691047
X-RAY DIFFRACTIONr_mcangle_it6.9018.5351303
X-RAY DIFFRACTIONr_mcangle_other6.8998.5361304
X-RAY DIFFRACTIONr_scbond_it7.5736.9251133
X-RAY DIFFRACTIONr_scbond_other7.5626.9211131
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.5139.9231617
X-RAY DIFFRACTIONr_long_range_B_refined12.67871.5842516
X-RAY DIFFRACTIONr_long_range_B_other12.67671.6012517
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å
RfactorNum. reflection% reflection
Rfree0.264 37 -
Rwork-700 -
obs--95.96 %

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