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- PDB-3dd9: Structure of DocH66Y dimer -

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Basic information

Entry
Database: PDB / ID: 3dd9
TitleStructure of DocH66Y dimer
ComponentsDeath on curing protein
KeywordsRIBOSOME INHIBITOR / all alpha
Function / homology
Function and homology information


killing by virus of host cell by post-segregational killing / symbiont-mediated suppression of host translation / regulation of translation / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / DNA binding / ATP binding
Similarity search - Function
PTS-regulatory domain, PRD - #50 / Helix Hairpins - #2060 / Death on curing protein / : / PTS-regulatory domain, PRD / Fic/DOC family / Fido domain / Fido domain profile. / Helix Hairpins / Helix non-globular ...PTS-regulatory domain, PRD - #50 / Helix Hairpins - #2060 / Death on curing protein / : / PTS-regulatory domain, PRD / Fic/DOC family / Fido domain / Fido domain profile. / Helix Hairpins / Helix non-globular / Special / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesEnterobacteria phage P1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsGarcia-Pino, A. / Loris, R.
CitationJournal: J. Biol. Chem. / Year: 2014
Title: The intrinsically disordered domain of the antitoxin Phd chaperones the toxin Doc against irreversible inactivation and misfolding
Authors: De Gieter, S. / Konijnenberg, A. / Talavera, A. / Butterer, A. / Haesaerts, S. / De Greve, H. / Sobott, F. / Loris, R. / Garcia-Pino, A.
History
DepositionJun 5, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 23, 2014Group: Other
Revision 1.3Mar 7, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.4Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Death on curing protein
B: Death on curing protein
C: Death on curing protein
D: Death on curing protein
E: Death on curing protein
F: Death on curing protein
G: Death on curing protein
H: Death on curing protein


Theoretical massNumber of molelcules
Total (without water)118,2608
Polymers118,2608
Non-polymers00
Water66737
1
A: Death on curing protein
B: Death on curing protein


Theoretical massNumber of molelcules
Total (without water)29,5652
Polymers29,5652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-44 kcal/mol
Surface area11520 Å2
MethodPISA
2
C: Death on curing protein
D: Death on curing protein


Theoretical massNumber of molelcules
Total (without water)29,5652
Polymers29,5652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-45 kcal/mol
Surface area11660 Å2
MethodPISA
3
E: Death on curing protein
F: Death on curing protein


Theoretical massNumber of molelcules
Total (without water)29,5652
Polymers29,5652
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-42 kcal/mol
Surface area10820 Å2
MethodPISA
4
G: Death on curing protein
H: Death on curing protein


Theoretical massNumber of molelcules
Total (without water)29,5652
Polymers29,5652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-44 kcal/mol
Surface area11800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.084, 197.988, 54.109
Angle α, β, γ (deg.)90.00, 93.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Death on curing protein


Mass: 14782.520 Da / Num. of mol.: 8 / Mutation: H66Y, E126D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P1 (virus) / Gene: doc / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q06259
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.4 Å3/Da / Density % sol: 48.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% PEG10000, 0.1M TRIS, pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8081 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 25, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8081 Å / Relative weight: 1
ReflectionResolution: 2.45→15 Å / Num. all: 40809 / Num. obs: 40809 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 44.3 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.7
Reflection shellResolution: 2.45→2.51 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3915

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Processing

Software
NameClassification
PHASERphasing
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DD7

3dd7


Resolution: 2.45→14.986 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 28.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2454 2026 5 %RANDOM
Rwork0.211 ---
obs0.2132 40500 99.7 %-
all-40809 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.942 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 52.2 Å2
Refinement stepCycle: LAST / Resolution: 2.45→14.986 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6818 0 0 37 6855
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0146909
X-RAY DIFFRACTIONf_angle_d1.5659390
X-RAY DIFFRACTIONf_dihedral_angle_d19.8592349
X-RAY DIFFRACTIONf_chiral_restr0.1111140
X-RAY DIFFRACTIONf_plane_restr0.011216
LS refinement shellResolution: 2.45→2.51 Å
RfactorNum. reflection
Rfree0.279 150
Rwork0.238 -
obs-2885

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