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- PDB-5i8j: Crystal structure of Dmd from phage RB69 -

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Basic information

Entry
Database: PDB / ID: 5i8j
TitleCrystal structure of Dmd from phage RB69
ComponentsDmd discriminator of mRNA degradation
KeywordsANTITOXIN
Function / homologyDiscriminator of mRNA degradation / Discriminator of mRNA degradation / Dmd discriminator of mRNA degradation
Function and homology information
Biological speciesEnterobacteria phage RB69 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsWei, Y. / Zhang, H. / Gao, Z.Q. / Dong, Y.H.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2016
Title: Structural characterizations of phage antitoxin Dmd and its interactions with bacterial toxin RnlA
Authors: Wei, Y. / Gao, Z.Q. / Zhang, H. / Dong, Y.H.
History
DepositionFeb 19, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dmd discriminator of mRNA degradation
B: Dmd discriminator of mRNA degradation


Theoretical massNumber of molelcules
Total (without water)14,7132
Polymers14,7132
Non-polymers00
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-8 kcal/mol
Surface area7440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.910, 53.933, 75.454
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Dmd discriminator of mRNA degradation


Mass: 7356.407 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage RB69 (virus) / Gene: dmd / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7Y599
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.21 Å3/Da / Density % sol: 44.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M HEPES 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 1W2B / Wavelength: 0.9792 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 13857 / % possible obs: 99.9 % / Redundancy: 13.7 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 53.76
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 11 % / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 8.81 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I8R

4i8r
PDB Unreleased entry


Resolution: 1.75→30.914 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.36
RfactorNum. reflection% reflection
Rfree0.223 668 4.88 %
Rwork0.1919 --
obs0.1934 13689 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.75→30.914 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1022 0 0 139 1161
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061040
X-RAY DIFFRACTIONf_angle_d0.9641395
X-RAY DIFFRACTIONf_dihedral_angle_d13.296377
X-RAY DIFFRACTIONf_chiral_restr0.046155
X-RAY DIFFRACTIONf_plane_restr0.004174
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7501-1.88520.27531170.21272550X-RAY DIFFRACTION100
1.8852-2.07490.21821400.18912547X-RAY DIFFRACTION100
2.0749-2.3750.24741380.19532562X-RAY DIFFRACTION100
2.375-2.99190.23331320.20862625X-RAY DIFFRACTION100
2.9919-30.9190.20051410.1792737X-RAY DIFFRACTION100

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