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- PDB-4osk: Crystal structure of TAL effector reveals the recognition between... -

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Basic information

Entry
Database: PDB / ID: 4osk
TitleCrystal structure of TAL effector reveals the recognition between asparagine and guanine
Components
  • DNA (5'-D(*AP*GP*TP*CP*TP*AP*GP*TP*AP*GP*TP*TP*GP*GP*AP*CP*A)-3')
  • DNA (5'-D(*TP*GP*TP*CP*CP*AP*AP*CP*TP*AP*CP*TP*AP*GP*AP*CP*T)-3')
  • Hax3
KeywordsDNA binding protein/DNA / DNA binding protein / DNA / DNA binding protein-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: 2.398 Å
AuthorsDeng, D. / Wu, J.P. / Yan, C.Y. / Pan, X.J. / Yan, N.
CitationJournal: Protein Cell / Year: 2014
Title: Revisiting the TALE repeat
Authors: Deng, D. / Yan, C.Y. / Wu, J.P. / Pan, X.J. / Yan, N.
History
DepositionFeb 13, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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*AP*AP*CP*TP*AP*CP*TP*AP*GP*AP*CP*T)-3')
J: DNA (5'-D(*AP*GP*TP*CP*TP*AP*GP*TP*AP*GP*TP*TP*GP*GP*AP*CP*A)-3')
B: Hax3
G: DNA (5'-D(*TP*GP*TP*CP*CP*AP*AP*CP*TP*AP*CP*TP*AP*GP*AP*CP*T)-3')
H: DNA (5'-D(*AP*GP*TP*CP*TP*AP*GP*TP*AP*GP*TP*TP*GP*GP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)124,5256
Polymers124,5256
Non-polymers00
Water4,684260
1
A: Hax3
I: DNA (5'-D(*TP*GP*TP*CP*CP*AP*AP*CP*TP*AP*CP*TP*AP*GP*AP*CP*T)-3')
J: DNA (5'-D(*AP*GP*TP*CP*TP*AP*GP*TP*AP*GP*TP*TP*GP*GP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)62,2623
Polymers62,2623
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-56 kcal/mol
Surface area23880 Å2
MethodPISA
2
B: Hax3
G: DNA (5'-D(*TP*GP*TP*CP*CP*AP*AP*CP*TP*AP*CP*TP*AP*GP*AP*CP*T)-3')
H: DNA (5'-D(*AP*GP*TP*CP*TP*AP*GP*TP*AP*GP*TP*TP*GP*GP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)62,2623
Polymers62,2623
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-50 kcal/mol
Surface area23580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.633, 88.129, 90.476
Angle α, β, γ (deg.)90.00, 104.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hax3


Mass: 51849.586 Da / Num. of mol.: 2 / Fragment: UNP residues 231-720
Mutation: N300H,I301D,I369S,H402N,D403S,H470N,D471G,N538H,S539D,S573G,H606N,D607S,I641N,G675S
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*AP*AP*CP*TP*AP*CP*TP*AP*GP*AP*CP*T)-3')


Mass: 5146.361 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*AP*GP*TP*CP*TP*AP*GP*TP*AP*GP*TP*TP*GP*GP*AP*CP*A)-3')


Mass: 5266.434 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.62 Å3/Da / Density % sol: 53.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 10%-15% PEG 3350, 12% ethanol, 0.1M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.39→40 Å / Num. all: 50310 / Num. obs: 50284 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 42.97 Å2

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Processing

Software
NameVersionClassification
HKL-2000data 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: 2.398→34.972 Å / FOM work R set: 0.7803 / SU ML: 0.61 / σ(F): 1.34 / Phase error: 28.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2551 2552 5.08 %
Rwork0.2144 47732 -
obs0.2164 50284 99.6 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.818 Å2 / ksol: 0.314 e/Å3
Displacement parametersBiso max: 160.5 Å2 / Biso mean: 53.89 Å2 / Biso min: 22.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.6647 Å20 Å2-9.3294 Å2
2---5.3742 Å2-0 Å2
3---6.0389 Å2
Refinement stepCycle: LAST / Resolution: 2.398→34.972 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7106 1362 0 260 8728
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0298735
X-RAY DIFFRACTIONf_angle_d1.10812193
X-RAY DIFFRACTIONf_chiral_restr0.0631494
X-RAY DIFFRACTIONf_plane_restr0.0071370
X-RAY DIFFRACTIONf_dihedral_angle_d22.4693301
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3982-2.44440.36191240.29512634275899
2.4444-2.49420.30271470.295226492796100
2.4942-2.54850.32021570.283326212778100
2.5485-2.60770.35521590.295626302789100
2.6077-2.67290.32451460.287826482794100
2.6729-2.74510.3291240.272526712795100
2.7451-2.82590.31771550.263126472802100
2.8259-2.91710.30811440.270326352779100
2.9171-3.02130.31311360.276426652801100
3.0213-3.14220.26321430.244926652808100
3.1422-3.28510.2921230.24726242747100
3.2851-3.45810.28361390.227626672806100
3.4581-3.67460.26651490.216926772826100
3.6746-3.95790.21941480.19332638278699
3.9579-4.35550.2381310.17542637276898
4.3555-4.98430.18761390.16442637277698
4.9843-6.27370.24021360.195226862822100
6.2737-34.97590.18761520.16092701285399
Refinement TLS params.Method: refined / Origin x: -35.6595 Å / Origin y: 12.7903 Å / Origin z: -19.926 Å
111213212223313233
T0.2677 Å20.0191 Å20.0211 Å2-0.2353 Å2-0.0006 Å2--0.2715 Å2
L0.5149 °20.0061 °20.2043 °2-0.2598 °20.0528 °2--0.537 °2
S0.0444 Å °0.1066 Å °-0.0118 Å °0.0174 Å °-0.0174 Å °0.0093 Å °-0.0059 Å °0.1228 Å °-0.0225 Å °
Refinement TLS groupSelection details: ALL

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