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- PDB-4gjr: Crystal structure of the TAL effector dHax3 bound to methylated dsDNA -

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Basic information

Entry
Database: PDB / ID: 4gjr
TitleCrystal structure of the TAL effector dHax3 bound to methylated dsDNA
Components
  • DNA (5'-D(*AP*GP*GP*GP*AP*GP*GP*TP*AP*GP*AP*GP*GP*GP*AP*CP*A)-3')
  • DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*(5CM)P*TP*AP*(5CM)P*CP*TP*CP*(5CM)P*CP*T)-3')
  • Hax3
KeywordsTRANSCRIPTION/DNA / transcription activator / DNA / nucleus / TRANSCRIPTION-DNA complex
Function / homology: / TAL effector repeat / TAL effector repeat / host cell nucleus / extracellular region / DNA / DNA (> 10) / Hax3
Function and homology information
Biological speciesXanthomonas campestris pv. armoraciae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsYan, N. / Deng, D. / Yan, C.Y. / Yin, P. / Pan, X.J. / Shi, Y.G.
CitationJournal: To be Published
Title: Crystal structure of a protein complex
Authors: Yan, N. / Deng, D. / Yan, C.Y. / Yin, P. / Pan, X.J. / Shi, Y.G.
History
DepositionAug 10, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: Hax3
I: DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*(5CM)P*TP*AP*(5CM)P*CP*TP*CP*(5CM)P*CP*T)-3')
J: DNA (5'-D(*AP*GP*GP*GP*AP*GP*GP*TP*AP*GP*AP*GP*GP*GP*AP*CP*A)-3')
B: Hax3
G: DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*(5CM)P*TP*AP*(5CM)P*CP*TP*CP*(5CM)P*CP*T)-3')
H: DNA (5'-D(*AP*GP*GP*GP*AP*GP*GP*TP*AP*GP*AP*GP*GP*GP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)124,4256
Polymers124,4256
Non-polymers00
Water14,988832
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16890 Å2
ΔGint-90 kcal/mol
Surface area45500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.839, 87.625, 88.455
Angle α, β, γ (deg.)90.00, 102.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hax3


Mass: 51754.508 Da / Num. of mol.: 2 / Fragment: TAL effector, UNP residues 231-720 / Mutation: multiple mutations
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. armoraciae (bacteria)
Gene: hax3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3ZD72
#2: DNA chain DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*(5CM)P*TP*AP*(5CM)P*CP*TP*CP*(5CM)P*CP*T)-3')


Mass: 5067.329 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic DNA oligos
#3: DNA chain DNA (5'-D(*AP*GP*GP*GP*AP*GP*GP*TP*AP*GP*AP*GP*GP*GP*AP*CP*A)-3')


Mass: 5390.510 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic DNA oligos
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 832 / 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: 2.49 Å3/Da / Density % sol: 50.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 10% PEG 3350, 14% ethanol, 0.1M MES pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.85→40 Å / Num. all: 104055 / Num. obs: 103243 / % possible obs: 99.22 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 27.73 Å2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V6T

3v6t


Resolution: 1.85→32.37 Å / Occupancy max: 1 / Occupancy min: 0.43 / SU ML: 0.49 / σ(F): 1.34 / Phase error: 23.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2297 5156 4.99 %RANDOM
Rwork0.1979 ---
all0.1995 104055 --
obs0.1995 103243 99.22 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.839 Å2 / ksol: 0.353 e/Å3
Displacement parametersBiso max: 117.24 Å2 / Biso min: 15.43 Å2
Baniso -1Baniso -2Baniso -3
1--0.8822 Å20 Å2-2.1959 Å2
2--0.598 Å2-0 Å2
3---0.9816 Å2
Refinement stepCycle: LAST / Resolution: 1.85→32.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7056 1387 0 832 9275
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098778
X-RAY DIFFRACTIONf_angle_d1.09612261
X-RAY DIFFRACTIONf_dihedral_angle_d19.4323265
X-RAY DIFFRACTIONf_chiral_restr0.071491
X-RAY DIFFRACTIONf_plane_restr0.0051375
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.849-1.870.32061400.2861282586
1.87-1.8920.31281440.2793289100
1.892-1.91510.30281710.26653336100
1.9151-1.93930.28351740.26083251100
1.9393-1.96480.29631800.25453303100
1.9648-1.99170.25151570.24313267100
1.9917-2.02020.27741520.23763282100
2.0202-2.05030.26731850.23483273100
2.0503-2.08240.2661710.2283280100
2.0824-2.11650.26061450.2263322100
2.1165-2.1530.27391740.21633328100
2.153-2.19210.25041740.22053228100
2.1921-2.23430.28631620.21453288100
2.2343-2.27990.25881850.20853295100
2.2799-2.32940.20292140.19833236100
2.3294-2.38360.22971800.19693284100
2.3836-2.44320.26261880.19643276100
2.4432-2.50920.21841810.2063281100
2.5092-2.5830.27251450.20483320100
2.583-2.66640.2531720.21513304100
2.6664-2.76160.24541980.20953269100
2.7616-2.87210.26691730.2153264100
2.8721-3.00280.24791830.21323293100
3.0028-3.16090.22731730.20463314100
3.1609-3.35880.23391800.20173291100
3.3588-3.61780.19141760.18173305100
3.6178-3.98130.19941830.16473288100
3.9813-4.5560.16821720.15353335100
4.556-5.73490.19431660.17383332100
5.7349-32.3750.2351580.1919312892
Refinement TLS params.Method: refined / Origin x: -35.0484 Å / Origin y: 14.6674 Å / Origin z: -18.744 Å
111213212223313233
T0.175 Å20.0211 Å20.0176 Å2-0.1542 Å20.0029 Å2--0.1728 Å2
L0.3622 °20.1305 °20.2007 °2-0.1629 °20.1536 °2--0.2861 °2
S0.0232 Å °0.0191 Å °-0.0017 Å °-0.0017 Å °0.0154 Å °-0.009 Å °-0.0029 Å °0.002 Å °-0.036 Å °
Refinement TLS groupSelection details: all

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