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- PDB-4zlx: N-terminal DNA binding domain of the antitoxin Phd from phage P1 -

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Basic information

Entry
Database: PDB / ID: 4zlx
TitleN-terminal DNA binding domain of the antitoxin Phd from phage P1
ComponentsAntitoxin phd
KeywordsTRANSCRIPTION / transcription factor / toxin-antitoxin / DNA binding / intrinsic disorder / conditional cooperativity
Function / homology
Function and homology information


toxin sequestering activity / DNA-binding transcription repressor activity / protein-DNA complex / sequence-specific DNA binding / negative regulation of DNA-templated transcription / protein homodimerization activity / DNA binding
Similarity search - Function
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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Antitoxin phd
Similarity search - Component
Biological speciesEnterobacteria phage P1 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsGarcia-Pino, A. / Loris, R.
CitationJournal: Nat.Chem.Biol. / Year: 2016
Title: An intrinsically disordered entropic switch determines allostery in Phd-Doc regulation.
Authors: Garcia-Pino, A. / De Gieter, S. / Talavera, A. / De Greve, H. / Efremov, R.G. / Loris, R.
History
DepositionMay 1, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2May 18, 2016Group: Database references
Revision 1.3Jun 29, 2016Group: Database references
Revision 1.4Jan 10, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Antitoxin phd
B: Antitoxin phd
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6357
Polymers12,3402
Non-polymers2955
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-15 kcal/mol
Surface area5070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.940, 42.940, 100.180
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Antitoxin phd / Addiction protein pdh / Prevent host death protein


Mass: 6169.816 Da / Num. of mol.: 2 / Fragment: UNP residues 1-45
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P1 (virus) / Gene: phd / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q06253
#2: Chemical
ChemComp-ACT / ACETATE ION


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


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 200 mM Lithium Sulfate monohydrate, 20% w/v PEG3350
PH range: 6.0 - 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.31→29.9 Å / Num. obs: 4518 / % possible obs: 97.3 % / Redundancy: 11.4 % / Biso Wilson estimate: 30.14 Å2 / Net I/σ(I): 57.8
Reflection shellResolution: 2.31→2.39 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 17.9 / % possible all: 86.7

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HS2

3hs2


Resolution: 2.31→29.86 Å / Cor.coef. Fo:Fc: 0.9335 / Cor.coef. Fo:Fc free: 0.8965 / SU R Cruickshank DPI: 0.329 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.338 / SU Rfree Blow DPI: 0.24 / SU Rfree Cruickshank DPI: 0.241
RfactorNum. reflection% reflectionSelection details
Rfree0.2452 211 5 %RANDOM
Rwork0.1787 ---
obs0.1817 4497 97.53 %-
Displacement parametersBiso mean: 32.74 Å2
Baniso -1Baniso -2Baniso -3
1--0.7423 Å20 Å20 Å2
2---0.7423 Å20 Å2
3---1.4845 Å2
Refine analyzeLuzzati coordinate error obs: 0.302 Å
Refinement stepCycle: LAST / Resolution: 2.31→29.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms715 0 20 55 790
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01753HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.191013HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d265SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes23HARMONIC2
X-RAY DIFFRACTIONt_gen_planes111HARMONIC5
X-RAY DIFFRACTIONt_it753HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.2
X-RAY DIFFRACTIONt_other_torsion20.27
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion100SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact935SEMIHARMONIC4
LS refinement shellResolution: 2.31→2.58 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2518 67 5.44 %
Rwork0.1702 1165 -
all0.1746 1232 -
obs--97.53 %
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)
15.87490.0272-2.96853.2026-1.45734.9776-0.374-0.3316-0.74850.06-0.2377-0.14360.5428-0.03410.6116-0.07430.05160.1191-0.16640.04110.0345-20.8251-2.414810.8436
26.71951.234-4.08981.55470.82593.7963-0.35140.6023-0.4009-0.364-0.0252-0.0043-0.0308-0.4310.37660.01690.00790.0252-0.0827-0.02190.0174-19.81152.85594.3883
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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