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- PDB-9k3e: DddB(BadTF3) dsDNA deaminase -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 9k3e
TitleDddB(BadTF3) dsDNA deaminase
Components
  • The immunity protein of DddB
  • YD repeat protein
KeywordsHYDROLASE / DsDNA deaminase
Function / homology
Function and homology information


Pput2613-like deaminase / Pput_2613-like deaminase / Bacteriophage T4 gp5 C-terminal trimerisation domain / Domain of unknown function DUF6531 / RHS protein / Domain of unknown function (DUF6531) / RHS protein / Type VI secretion system, RhsGE-associated Vgr family subset / Type VI secretion system, RhsGE-associated Vgr protein / RHS repeat ...Pput2613-like deaminase / Pput_2613-like deaminase / Bacteriophage T4 gp5 C-terminal trimerisation domain / Domain of unknown function DUF6531 / RHS protein / Domain of unknown function (DUF6531) / RHS protein / Type VI secretion system, RhsGE-associated Vgr family subset / Type VI secretion system, RhsGE-associated Vgr protein / RHS repeat / RHS Repeat / Phage tail baseplate hub (GPD) / YD repeat / Gp5/Type VI secretion system Vgr protein, OB-fold domain / Type VI secretion system/phage-baseplate injector OB domain / Vgr protein, OB-fold domain superfamily / Rhs repeat-associated core / :
Similarity search - Domain/homology
YD repeat protein / Uncharacterized protein
Similarity search - Component
Biological speciesTaylorella equigenitalis
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDong, W.Y. / Xiaoliang, S.X.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: Genome-wide mapping of human transcription factors' footprints with double-stranded DNA deaminase
Authors: Wenyang, D. / Xiaoliang, S.X.
History
DepositionOct 18, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: YD repeat protein
C: The immunity protein of DddB


Theoretical massNumber of molelcules
Total (without water)28,7332
Polymers28,7332
Non-polymers00
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-7 kcal/mol
Surface area11840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.069, 130.646, 61.618
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein YD repeat protein


Mass: 15227.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Taylorella equigenitalis (strain MCE9) (bacteria)
Gene: TEQUI_0434 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A654KG07
#2: Protein The immunity protein of DddB


Mass: 13505.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Taylorella equigenitalis (strain MCE9) (bacteria)
Gene: TEQUI_0433 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A654KG21
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
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: 2.94 Å3/Da / Density % sol: 58.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 10% (w/v) PEG 8000, 100 mM Potassium phosphate monobasic/ Sodium phosphate dibasic, 200 mM Sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.5418 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Dec 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→12.62 Å / Num. obs: 11988 / % possible obs: 99.94 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.025 / Rrim(I) all: 0.079 / Net I/σ(I): 25.4
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.298 / Num. unique obs: 1175 / Rpim(I) all: 0.101 / Rrim(I) all: 0.315

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
PHENIXphasing
CrysalisProdata reduction
CrysalisProdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→12.62 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2396 1197 10 %
Rwork0.1944 --
obs0.1988 11971 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→12.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1780 0 0 82 1862
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081815
X-RAY DIFFRACTIONf_angle_d0.9662457
X-RAY DIFFRACTIONf_dihedral_angle_d7.724242
X-RAY DIFFRACTIONf_chiral_restr0.058274
X-RAY DIFFRACTIONf_plane_restr0.007320
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.60.27711310.21741181X-RAY DIFFRACTION99
2.6-2.720.34241300.22081173X-RAY DIFFRACTION100
2.72-2.860.25491310.23661174X-RAY DIFFRACTION100
2.86-3.030.26151320.23811184X-RAY DIFFRACTION100
3.04-3.270.27741320.2131188X-RAY DIFFRACTION100
3.27-3.590.25141320.19521191X-RAY DIFFRACTION100
3.59-4.090.23951350.17881210X-RAY DIFFRACTION100
4.09-5.10.191330.16311204X-RAY DIFFRACTION100
5.1-12.620.20311410.18211269X-RAY DIFFRACTION100

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