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- PDB-7ycw: Crystal Form 1 of Truncated Antitoxin ParD (2-54,containg RHH dom... -

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Basic information

Entry
Database: PDB / ID: 7ycw
TitleCrystal Form 1 of Truncated Antitoxin ParD (2-54,containg RHH domain) from Pseudoalteromonas rubra
ComponentsAntitoxin ParD
KeywordsANTITOXIN / RHH / Transcription Factor / Toxin antitoxin system
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: 2.2 Å
AuthorsWang, C.C. / Niu, C.Y. / Niu, L.W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) 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
C: Antitoxin ParD
D: Antitoxin ParD
A: Antitoxin ParD
B: Antitoxin ParD


Theoretical massNumber of molelcules
Total (without water)28,2684
Polymers28,2684
Non-polymers00
Water1,18966
1
C: Antitoxin ParD
D: Antitoxin ParD
A: Antitoxin ParD
B: Antitoxin ParD

C: Antitoxin ParD
D: Antitoxin ParD
A: Antitoxin ParD
B: Antitoxin ParD

C: Antitoxin ParD
D: Antitoxin ParD
A: Antitoxin ParD
B: Antitoxin ParD

C: Antitoxin ParD
D: Antitoxin ParD
A: Antitoxin ParD
B: Antitoxin ParD


Theoretical massNumber of molelcules
Total (without water)113,07016
Polymers113,07016
Non-polymers00
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area44550 Å2
ΔGint-201 kcal/mol
Surface area35970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.836, 61.836, 129.971
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Space group name HallP4n2n
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/2
#3: y+1/2,-x+1/2,z+1/2
#4: x+1/2,-y+1/2,-z+1/2
#5: -x+1/2,y+1/2,-z+1/2
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z

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Components

#1: Protein
Antitoxin ParD


Mass: 7066.906 Da / Num. of mol.: 4
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.: 66 / 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: 2.2 Å3/Da / Density % sol: 44.03 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M Sodium acetate trihydrate,0.1 M Sodium citrate pH 5.5, 5 % w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.2→30.78 Å / Num. obs: 13454 / % possible obs: 99.71 % / Observed criterion σ(I): 3 / Redundancy: 24.1 % / Biso Wilson estimate: 43.48 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.06929 / Rpim(I) all: 0.01471 / Rrim(I) all: 0.07089 / Net I/σ(I): 30.41
Reflection shellResolution: 2.2→2.279 Å / Redundancy: 25.8 % / Rmerge(I) obs: 0.601 / Mean I/σ(I) obs: 5.95 / Num. unique obs: 1294 / CC1/2: 0.989 / CC star: 0.997 / Rpim(I) all: 0.1194 / Rrim(I) all: 0.613 / % possible all: 98.92

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSFeb 5, 2021 BUILT=20210323data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7B22

7b22


Resolution: 2.2→30.78 Å / SU ML: 0.2369 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.1627
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2486 665 4.95 %
Rwork0.2189 12773 -
obs0.2204 13438 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.42 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1608 0 0 66 1674
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00791612
X-RAY DIFFRACTIONf_angle_d0.96142158
X-RAY DIFFRACTIONf_chiral_restr0.0505260
X-RAY DIFFRACTIONf_plane_restr0.0057278
X-RAY DIFFRACTIONf_dihedral_angle_d15.3664618
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.370.30591350.28742468X-RAY DIFFRACTION99.47
2.37-2.610.28071250.2372508X-RAY DIFFRACTION99.85
2.61-2.980.30831330.25592506X-RAY DIFFRACTION99.92
2.99-3.760.24591310.22132563X-RAY DIFFRACTION99.93
3.76-30.780.21891410.19572728X-RAY DIFFRACTION99.9

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