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

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Basic information

Entry
Database: PDB / ID: 4osj
TitleCrystal structure of TAL effector reveals the recognition between asparagine and adenine
Components
  • DNA (5'-D(*AP*GP*AP*GP*AP*GP*AP*TP*AP*AP*AP*GP*GP*GP*AP*CP*A)-3')
  • DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*TP*AP*TP*CP*TP*CP*TP*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: 2.79 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*CP*TP*TP*TP*AP*TP*CP*TP*CP*TP*CP*T)-3')
J: DNA (5'-D(*AP*GP*AP*GP*AP*GP*AP*TP*AP*AP*AP*GP*GP*GP*AP*CP*A)-3')
B: Hax3
G: DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*TP*AP*TP*CP*TP*CP*TP*CP*T)-3')
H: DNA (5'-D(*AP*GP*AP*GP*AP*GP*AP*TP*AP*AP*AP*GP*GP*GP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)124,3896
Polymers124,3896
Non-polymers00
Water70339
1
A: Hax3
I: DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*TP*AP*TP*CP*TP*CP*TP*CP*T)-3')
J: DNA (5'-D(*AP*GP*AP*GP*AP*GP*AP*TP*AP*AP*AP*GP*GP*GP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)62,1943
Polymers62,1943
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-62 kcal/mol
Surface area23050 Å2
MethodPISA
2
B: Hax3
G: DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*TP*AP*TP*CP*TP*CP*TP*CP*T)-3')
H: DNA (5'-D(*AP*GP*AP*GP*AP*GP*AP*TP*AP*AP*AP*GP*GP*GP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)62,1943
Polymers62,1943
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-66 kcal/mol
Surface area23380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.413, 80.807, 88.821
Angle α, β, γ (deg.)90.00, 103.68, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hax3


Mass: 51781.531 Da / Num. of mol.: 2 / Fragment: UNP residues 231-720
Mutation: N300H,I301D,N368H,I369D,H402N,D403G,H436N,D437G,H470N,D471G,S505N,S539G,N572H,S573D,H606N,D607G,N640H,I641D
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*TP*TP*AP*TP*CP*TP*CP*TP*CP*T)-3')


Mass: 5070.281 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*AP*GP*AP*GP*AP*GP*AP*TP*AP*AP*AP*GP*GP*GP*AP*CP*A)-3')


Mass: 5342.513 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.37 Å3/Da / Density % sol: 48.02 %
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 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.79→40 Å / Num. all: 28532 / Num. obs: 28507 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 46.22 Å2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V6T

3v6t


Resolution: 2.79→38.064 Å / FOM work R set: 0.7484 / SU ML: 0.37 / σ(F): 1.35 / Phase error: 31.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2709 1443 5.06 %
Rwork0.2136 27064 -
obs0.2166 28507 98.05 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.491 Å2 / ksol: 0.303 e/Å3
Displacement parametersBiso max: 149.52 Å2 / Biso mean: 54.89 Å2 / Biso min: 21.89 Å2
Baniso -1Baniso -2Baniso -3
1--10.5222 Å2-0 Å2-10.081 Å2
2---1.4716 Å20 Å2
3---15.5013 Å2
Refinement stepCycle: LAST / Resolution: 2.79→38.064 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7046 1305 0 39 8390
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098605
X-RAY DIFFRACTIONf_angle_d1.40212004
X-RAY DIFFRACTIONf_chiral_restr0.0821471
X-RAY DIFFRACTIONf_plane_restr0.0091359
X-RAY DIFFRACTIONf_dihedral_angle_d21.5953240
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.79-2.88970.36541290.30052411254089
2.8897-3.00540.36671340.28862536267092
3.0054-3.14210.35791560.263227242880100
3.1421-3.30770.35621470.250827362883100
3.3077-3.51480.27371210.221528002921100
3.5148-3.78590.27291550.206827172872100
3.7859-4.16650.24321410.189927742915100
4.1665-4.76840.22781430.169927742917100
4.7684-6.00390.27291480.222227802928100
6.0039-38.06760.2191690.190828122981100
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)
10.72780.0828-0.08880.7502-0.2140.37490.0416-0.2167-0.14770.1755-0.02290.00750.0139-0.0234-0.00690.2519-0.012-0.0510.3420.0660.316220.7318-18.934-4.8917
21.09550.09780.25330.41140.12080.36940.0217-0.0889-0.0437-0.0185-0.03040.09840.016-0.0732-0.02560.2623-0.0054-0.03170.2440.02490.3165-12.3883-11.9679-39.5708
32.0062-0.1348-0.62351.88220.18320.23410.19180.16290.12590.03710.16020.0993-0.049-0.09630.0060.3420.0047-0.04670.42030.02940.3642-7.9783-9.4821-47.0915
42.21970.60430.7442.0347-0.97661.92170.21210.28370.4418-0.25490.172-0.1296-0.0408-0.08050.0180.39610.02760.06060.56970.06020.416-6.9564-7.2932-47.0689
52.1818-0.1186-0.34691.845-0.60520.6233-0.1317-0.1644-0.2802-0.2307-0.0055-0.08140.0256-0.3314-0.00060.3987-0.061-0.05930.4918-0.0220.351925.6647-15.2997-5.9768
62.39360.10480.48741.13380.12361.9941-0.1084-0.4047-0.4966-0.2799-0.0057-0.2994-0.05110.0189-0.02430.4694-0.0589-0.16180.47620.01820.677727.5262-16.5813-7.0206
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN G
4X-RAY DIFFRACTION4CHAIN H
5X-RAY DIFFRACTION5CHAIN I
6X-RAY DIFFRACTION6CHAIN J

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