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- PDB-3k33: Crystal structure of the Phd-Doc complex -

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Basic information

Entry
Database: PDB / ID: 3k33
TitleCrystal structure of the Phd-Doc complex
Components
  • Death on curing protein
  • Polypeptide of unknown amino acids and source
  • Prevent host death protein
KeywordsTOXIN/ANTITOXIN / Phd / Doc / Fic / toxin / antitoxin / intrinsic disorder / allostery / transcription regulation / ribosome inhibitor / TOXIN-ANTITOXIN COMPLEX
Function / homology
Function and homology information


killing by virus of host cell by post-segregational killing / symbiont-mediated suppression of host translation / toxin sequestering activity / DNA-binding transcription repressor activity / protein-DNA complex / regulation of translation / sequence-specific DNA binding / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity ...killing by virus of host cell by post-segregational killing / symbiont-mediated suppression of host translation / toxin sequestering activity / DNA-binding transcription repressor activity / protein-DNA complex / regulation of translation / sequence-specific DNA binding / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / negative regulation of DNA-templated transcription / protein homodimerization activity / DNA binding / ATP binding
Similarity search - Function
Fic/DOC protein, Fido domain / Death on curing protein / : / YefM-like domain / Type II toxin-antitoxin system, antitoxin Phd/YefM / Antitoxin Phd_YefM, type II toxin-antitoxin system / YefM-like superfamily / YefM-like fold / Fic/DOC family / Fido domain ...Fic/DOC protein, Fido domain / Death on curing protein / : / YefM-like domain / Type II toxin-antitoxin system, antitoxin Phd/YefM / Antitoxin Phd_YefM, type II toxin-antitoxin system / YefM-like superfamily / YefM-like fold / Fic/DOC family / Fido domain / Fido domain profile. / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Antitoxin phd / Protein kinase doc
Similarity search - Component
Biological speciesEnterobacteria phage P1 (virus)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLoris, R. / Garcia-Pino, A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2010
Title: Allostery and intrinsic disorder mediate transcription regulation by conditional cooperativity.
Authors: Garcia-Pino, A. / Balasubramanian, S. / Wyns, L. / Gazit, E. / De Greve, H. / Magnuson, R.D. / Charlier, D. / van Nuland, N.A. / Loris, R.
History
DepositionOct 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
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.db_align_beg / _struct_ref_seq.db_align_end / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: Prevent host death protein
C: Prevent host death protein
D: Prevent host death protein
E: Polypeptide of unknown amino acids and source
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1907
Polymers39,0725
Non-polymers1182
Water3,369187
1
A: Death on curing protein
B: Prevent host death protein
C: Prevent host death protein
D: Prevent host death protein
hetero molecules

A: Death on curing protein
B: Prevent host death protein
C: Prevent host death protein
D: Prevent host death protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,30112
Polymers76,0658
Non-polymers2364
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
MethodPISA
2
E: Polypeptide of unknown amino acids and source


Theoretical massNumber of molelcules
Total (without water)1,0391
Polymers1,0391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.295, 48.295, 347.321
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11D-138-

HOH

DetailsThe biological unit is a heterooctamer consisting of a linear array with architecture Phd-Phd-Doc-Phd-Phd-Doc-Phd-Phd

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Components

#1: Protein Death on curing protein


Mass: 13603.252 Da / Num. of mol.: 1
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: Protein Prevent host death protein


Mass: 8143.076 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P1 (virus) / Gene: phd / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q06253
#3: Protein/peptide Polypeptide of unknown amino acids and source


Mass: 1039.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Production host: unidentified (others)
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.99 Å3/Da / Density % sol: 58.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 100 mM Sodium acetate pH 4.5, 20 mM CaCl2 and 35-40% v/v MPD, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.934 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 19, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.4→42 Å / Num. obs: 19121 / % possible obs: 100 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 23.2
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.224 / Mean I/σ(I) obs: 10.8 / Rsym value: 0.224 / % possible all: 97.8

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Processing

Software
NameClassification
MAR345dtbdata collection
PHASERphasing
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3DD7

3dd7


Resolution: 2.4→41.825 Å / SU ML: 1.76 / σ(F): 0.16 / Phase error: 25.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2848 965 5.05 %
Rwork0.2569 --
obs0.2583 19121 97.39 %
all-19121 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.973 Å2 / ksol: 0.297 e/Å3
Refinement stepCycle: LAST / Resolution: 2.4→41.825 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2447 0 8 187 2642
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092478
X-RAY DIFFRACTIONf_angle_d1.2663349
X-RAY DIFFRACTIONf_dihedral_angle_d18.39848
X-RAY DIFFRACTIONf_chiral_restr0.233387
X-RAY DIFFRACTIONf_plane_restr0.004456
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.52650.31481340.25152464X-RAY DIFFRACTION96
2.5265-2.68480.26611320.24752537X-RAY DIFFRACTION97
2.6848-2.8920.28971480.25442480X-RAY DIFFRACTION97
2.892-3.1830.26461280.25312591X-RAY DIFFRACTION98
3.183-3.64330.311360.24032592X-RAY DIFFRACTION97
3.6433-4.58930.24951350.22622633X-RAY DIFFRACTION98
4.5893-41.8310.28891520.28392859X-RAY DIFFRACTION98
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1refined4.89990.9644-1.47291.8857-1.29416.5756-0.527-0.1301-0.57530.3020.4518-0.41110.9549-0.348-0.26090.17110.08910.00440.10730.08420.1069-26.52-5.357351.5294
20.998-0.1329-0.02280.65410.70663.07610.3240.0544-0.2053-0.0680.3265-0.16080.0741-0.8174-0.50220.2090.02960.08020.33080.16490.328
31.4244-1.34090.24572.5510.51280.74130.06370.13230.1010.27110.0665-0.25820.07530.3175-0.1030.159-0.0313-0.01420.15410.01650.1648
40.1441-0.8546-0.02231.4576-0.5669-0.07820.10050.02950.22210.24850.0350.21910.1497-0.0484-0.07660.16250.03310.01750.18530.0140.154
51.29110.68520.14470.9563-0.1011.427-0.0494-0.28250.3575-0.13320.11610.3153-0.4137-0.0879-0.07860.16030.077-0.02110.1277-0.0430.1379
60.6721-0.28650.07710.439-0.97211.2997-0.18610.06890.3405-0.05970.17730.0712-0.8467-0.10460.05670.30930.05370.01910.23950.02640.2923
76.82411.76042.6058-1.7491-3.0753-0.91661.7193-1.69-1.53711.5783-0.94860.0831-1.2034-0.4362-0.69321.13450.13180.0430.72430.14630.5174
80.395-0.04160.64242.79160.65391.33830.75830.38731.71841.5350.04750.4385-0.18220.2761-0.4020.550.07410.01970.54530.05830.6241
90.4147-0.5278-0.05673.5781-1.28870.6938-0.2726-0.2315-0.02121.3380.1440.0406-0.6193-0.1320.11720.32860.14140.0910.23580.07050.2066
103.3271.0162-0.5122.1852-0.42170.7539-0.44090.4495-0.30660.38690.33870.979-0.5185-0.3177-0.06490.22320.16670.04930.33710.1330.3901
116.3297-1.86580.40891.3883-0.11592.29480.45720.2209-1.63710.0617-0.23820.60370.27370.152-0.07310.09670.0149-0.04180.0845-0.11010.3712
121.0626-0.0956-1.12861.8130.69180.99430.25240.3481-0.5368-0.4324-0.26960.1805-0.03520.0183-0.20220.13730.0627-0.11230.0987-0.05550.1839
130.0469-0.55290.76670.39531.1707-0.33750.0153-0.05630.0502-0.10320.0129-0.2016-0.07750.0121-0.05250.1182-0.00960.00980.17370.02470.105
141.53960.0044-0.36171.2032-0.804-0.63070.46181.60110.1171-2.78021.41350.3674-0.1835-0.6265-1.22230.8165-0.0747-0.14520.8408-0.1090.5036
158.3354-1.18150.8612.01010.81485.5583-0.2468-1.5221-1.1628-0.08440.22830.6354-0.9590.65780.27680.77360.3340.0111.3073-0.1060.6494
166.6933-0.413-0.4208-0.53-0.03046.87110.50860.7590.9696-0.146-0.3211-1.63631.54761.3215-0.18940.60970.1784-0.05090.5280.00740.4085
173.85530.5324-0.10714.22030.03923.1509-1.0893-0.3814-0.67221.2780.69321.44060.5527-0.07530.57030.56640.19610.30440.54040.08130.7813
184.5043-1.5026-1.20961.7345-0.0356-1.94450.3027-0.0236-0.24241.60280.2233-0.2135-0.36080.2832-0.5130.93860.09440.06720.5568-0.06040.2273
194.17231.2333-1.12910.8671.74672.07810.8463-0.72520.83930.24571.4381-0.05820.03970.2067-1.62850.81970.0568-0.27780.53990.1050.4795
201.01520.5205-0.14091.80710.14460.45221.0728-0.8065-0.4475-1.4065-0.4262-1.33421.1442-1.0719-0.27892.49810.3772-0.27370.8990.22840.417
213.01531.5544-3.51090.8797-0.10762.0013-0.7128-0.67560.07980.1691-0.1840.54181.89411.19880.51220.5358-0.2863-0.06230.90660.08020.2923
Refinement TLS groupSelection details: chain E

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