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- PDB-7ycv: The Dimeric Format of Truncated PrpA (2-54)and RHH Domain of PrpA -

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Basic information

Entry
Database: PDB / ID: 7ycv
TitleThe Dimeric Format of Truncated PrpA (2-54)and RHH Domain of PrpA
ComponentsAntitoxin ParD
KeywordsANTITOXIN / Toxin antitoxin system / RHH Transcription factor / ParD_antitoxin / Pseudoalteromonas rubra / ANTIMICROBIAL PROTEIN
Function / homologyBacterial antitoxin of ParD toxin-antitoxin type II system and RHH / Antitoxin ParD / Antitoxin ParD superfamily / Ribbon-helix-helix / regulation of DNA-templated transcription / Antitoxin ParD
Function and homology information
Biological speciesPseudoalteromonas rubra (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsWang, C.C. / Niu, C.Y. / Niu, L.W.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Front Microbiol / Year: 2022
Title: Structural insights into the PrpTA toxin-antitoxin system in Pseudoalteromonas rubra.
Authors: Wang, C. / Niu, C. / Hidayatullah, K.M. / Xue, L. / Zhu, Z. / Niu, L.
History
DepositionJul 1, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Antitoxin ParD
B: Antitoxin ParD


Theoretical massNumber of molelcules
Total (without water)14,1342
Polymers14,1342
Non-polymers00
Water543
1
A: Antitoxin ParD
B: Antitoxin ParD
x 8


Theoretical massNumber of molelcules
Total (without water)113,07016
Polymers113,07016
Non-polymers00
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area47820 Å2
ΔGint-218 kcal/mol
Surface area37790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.252, 83.252, 70.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

#1: Protein Antitoxin ParD


Mass: 7066.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas rubra (bacteria) / Gene: AT705_24525 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0U3H4C4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.17 Å3/Da / Density % sol: 43.32 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M HEPES sodium pH 7.5, 30 % v/v PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Dec 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.61→30.34 Å / Num. obs: 3976 / % possible obs: 99.25 % / Redundancy: 13.7 % / Biso Wilson estimate: 62.7 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.1038 / Rpim(I) all: 0.02865 / Rrim(I) all: 0.108 / Net I/σ(I): 16.46
Reflection shellResolution: 2.612→2.706 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.8511 / Mean I/σ(I) obs: 2.99 / Num. unique obs: 373 / CC1/2: 0.907 / CC star: 0.975 / Rpim(I) all: 0.2309 / Rrim(I) all: 0.8837 / % possible all: 97.9

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Processing

Software
NameVersionClassification
Coot0.9.6model building
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7B22

7b22


Resolution: 2.61→30.34 Å / SU ML: 0.2446 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.9639
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2714 188 4.73 %
Rwork0.2276 3786 -
obs0.2297 3974 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.88 Å2
Refinement stepCycle: LAST / Resolution: 2.61→30.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms846 0 0 3 849
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0119850
X-RAY DIFFRACTIONf_angle_d1.44451138
X-RAY DIFFRACTIONf_chiral_restr0.091135
X-RAY DIFFRACTIONf_plane_restr0.0091147
X-RAY DIFFRACTIONf_dihedral_angle_d15.2971326
LS refinement shellResolution: 2.61→2.706 Å
RfactorNum. reflection% reflection
Rfree0.2714 188 -
Rwork0.2276 3786 -
obs--99.37 %

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