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- PDB-3dd7: Structure of DocH66Y in complex with the C-terminal domain of Phd -

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Basic information

Entry
Database: PDB / ID: 3dd7
TitleStructure of DocH66Y in complex with the C-terminal domain of Phd
Components
  • Death on curing protein
  • Prevent host death 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 / toxin sequestering activity / DNA-binding transcription repressor activity / protein-DNA complex / sequence-specific DNA binding / non-specific serine/threonine protein kinase / phosphorylation / protein serine 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 / sequence-specific DNA binding / non-specific serine/threonine protein kinase / phosphorylation / 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 / Type II toxin-antitoxin system, antitoxin Phd/YefM / Antitoxin Phd_YefM, type II toxin-antitoxin system / YefM-like superfamily / Fido domain / Fic/DOC family / Fido domain profile. / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
BROMIDE ION / Antitoxin phd / Protein kinase doc
Similarity search - Component
Biological speciesEnterobacteria phage P1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsGarcia-Pino, A. / Loris, R.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Doc of Prophage P1 Is Inhibited by Its Antitoxin Partner Phd through Fold Complementation
Authors: Garcia-Pino, A. / Christensen-Dalsgaard, M. / Wyns, L. / Yarmolinsky, M. / Magnuson, R.D. / Gerdes, K. / Loris, R.
History
DepositionJun 5, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / struct_conn / struct_ref_seq_dif / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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: Death on curing protein
D: Prevent host death protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,11720
Polymers34,8384
Non-polymers1,27816
Water4,107228
1
A: Death on curing protein
B: Prevent host death protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,21812
Polymers17,4192
Non-polymers79910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-12.7 kcal/mol
Surface area6030 Å2
MethodPISA
2
C: Death on curing protein
D: Prevent host death protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8998
Polymers17,4192
Non-polymers4796
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-10.1 kcal/mol
Surface area6340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.944, 38.201, 63.734
Angle α, β, γ (deg.)90.00, 99.26, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Death on curing protein / DOC


Mass: 14782.520 Da / Num. of mol.: 2 / 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: Protein/peptide Prevent host death protein / PHD


Mass: 2636.724 Da / Num. of mol.: 2
Fragment: Prevent host death protein C-terminal domain, UNP residues 51-73
Mutation: L70(MSE) / Source method: obtained synthetically / Details: peptide Alta Bioscience / References: UniProt: Q06253
#3: Chemical
ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 1.91 Å3/Da / Density % sol: 35.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 35% PEG4000, 0.2M ammonium acetate, 0.1M acetate, pH4.6, 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: X12 / Wavelength: 0.9189, 0.9116
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 19, 2007
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91891
20.91161
ReflectionResolution: 1.7→11 Å / Num. all: 29371 / Num. obs: 29371 / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 19.4 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→11 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.485 / SU ML: 0.069 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.105
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19849 1444 5.1 %RANDOM
Rwork0.18232 ---
all0.18317 26810 --
obs0.18317 26810 96.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.801 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å2-0.06 Å2
2--0.57 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.7→11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2119 0 16 228 2363
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222257
X-RAY DIFFRACTIONr_angle_refined_deg1.2371.9693092
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.765324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.41923.40494
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.83415370
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7231519
X-RAY DIFFRACTIONr_chiral_restr0.0790.2369
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021718
X-RAY DIFFRACTIONr_nbd_refined0.2180.21238
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21625
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2182
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2640.228
X-RAY DIFFRACTIONr_mcbond_it0.641.51513
X-RAY DIFFRACTIONr_mcangle_it1.02222365
X-RAY DIFFRACTIONr_scbond_it1.9873829
X-RAY DIFFRACTIONr_scangle_it2.9394.5705
LS refinement shellResolution: 1.7→1.743 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 71 -
Rwork0.329 1522 -
obs-1451 75.25 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
13.98853.90882.82016.79343.70032.485-0.0121-0.18910.13210.0376-0.04460.2289-0.052-0.08830.0567-0.06760.00310.0126-0.1080.0087-0.06468.7352.266-11.196
23.50161.7919-2.03973.1768-1.96513.40310.0399-0.0897-0.0210.0513-0.03350.05760.0406-0.0487-0.0064-0.0736-0.0218-0.0187-0.10730.0088-0.0576.552-10.237-18.36
31.2630.790.22392.65971.20372.5208-0.0439-0.13920.0010.08820.01540.0030.0375-0.03480.0285-0.07110.01940.007-0.1089-0.0098-0.087315.9832.977-1.843
42.21441.7780.3732.58240.47341.63170.0551-0.0731-0.13870.0620.012-0.070.0522-0.0334-0.0671-0.07930.0049-0.0021-0.1160.0092-0.070316.532-5.926-11.526
50.86131.3231-0.25113.02480.82813.32010.00710.00550.1604-0.11450.05810.1813-0.1954-0.0327-0.0652-0.0549-0.0045-0.0067-0.12320.0121-0.074617.7125.561-18.537
61.90450.1737-0.41342.20950.06482.16430.0008-0.0385-0.0708-0.00630.0316-0.056-0.0340.1871-0.0324-0.0991-0.0047-0.0072-0.11890.0007-0.071427.303-3.02-15.19
76.8496-2.11060.85445.6-2.04353.51460.04240.0342-0.0104-0.02460.081-0.03290.022-0.0024-0.1235-0.0421-0.01080.0031-0.11620.0017-0.108214.484-3.453-25.58
80.5867-0.7096-1.37132.0041.90123.376-0.0333-0.0912-0.15750.0103-0.00380.05090.17020.01160.0371-0.0748-0.0152-0.0098-0.10510.0046-0.0716-15.997.236-13.699
92.4822-0.7468-0.3683.8573-1.2632.12670.0168-0.0154-0.1629-0.1533-0.031-0.0310.19870.04890.0142-0.0428-0.00820.003-0.1033-0.0268-0.0729-8.773.297-25.914
100.8288-0.0493-0.68392.0531.31012.73440.0068-0.0884-0.01920.07550.025-0.18420.05950.1376-0.0318-0.0821-0.018-0.0016-0.09140.0216-0.0687-9.0098.389-3.625
110.7398-0.5955-0.07063.24711.68042.44150.02370.0536-0.0577-0.03060.0027-0.11590.05780.0545-0.0264-0.0792-0.02450.0027-0.12440.0057-0.0712-4.6359.338-15.774
121.98910.3758-1.26131.03270.77922.80930.00090.00760.0375-0.0297-0.02090.0553-0.1267-0.04740.02-0.0618-0.0139-0.0082-0.12770.0023-0.0769-14.32718.873-15.93
132.6090.26220.07451.49250.70721.52220.0002-0.03410.06580.0207-0.0421-0.1212-0.06450.0810.042-0.0641-0.03060.0039-0.13560.0091-0.0637-1.12820.602-14.637
148.27840.48560.7891.01250.15931.9538-0.02190.2382-0.2216-0.1387-0.0835-0.0179-0.0108-0.0770.1055-0.0424-0.0038-0.0003-0.1208-0.0046-0.0884-13.25514.768-25.983
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 121 - 12
2X-RAY DIFFRACTION2AA13 - 2913 - 29
3X-RAY DIFFRACTION3AA30 - 5130 - 51
4X-RAY DIFFRACTION4AA52 - 7752 - 77
5X-RAY DIFFRACTION5AA78 - 9378 - 93
6X-RAY DIFFRACTION6AA94 - 12394 - 123
7X-RAY DIFFRACTION7BB54 - 714 - 21
8X-RAY DIFFRACTION8CC1 - 121 - 12
9X-RAY DIFFRACTION9CC13 - 2913 - 29
10X-RAY DIFFRACTION10CC30 - 5130 - 51
11X-RAY DIFFRACTION11CC52 - 7752 - 77
12X-RAY DIFFRACTION12CC78 - 9378 - 93
13X-RAY DIFFRACTION13CC94 - 12394 - 123
14X-RAY DIFFRACTION14DD51 - 721 - 22

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