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- PDB-4osm: Crystal structure of the S505H mutant of TAL effector dHax3 -

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Basic information

Entry
Database: PDB / ID: 4osm
TitleCrystal structure of the S505H mutant of TAL effector dHax3
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: 2.454 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
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')
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)124,4376
Polymers124,4376
Non-polymers00
Water4,594255
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)62,2183
Polymers62,2183
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-67 kcal/mol
Surface area23590 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)62,2183
Polymers62,2183
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-58 kcal/mol
Surface area24640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.191, 87.449, 87.967
Angle α, β, γ (deg.)90.00, 102.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hax3


Mass: 51805.574 Da / Num. of mol.: 2 / Fragment: UNP residues 231-720
Mutation: N300H,I301D,N368H,I369D,H402N,D403G,H436N,D437G,H470N,D471G,S505H,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.: 255 / 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: 2.45 Å3/Da / Density % sol: 49.76 %
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 / Wavelength: 0.9785 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.45→41.77 Å / Num. all: 44029 / Num. obs: 44006 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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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: 2.454→41.769 Å / FOM work R set: 0.7944 / SU ML: 0.44 / σ(F): 1.34 / Phase error: 27.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2573 2218 5.04 %RANDOM
Rwork0.215 41788 --
obs0.2171 44006 99.83 %-
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 15.718 Å2 / ksol: 0.307 e/Å3
Displacement parametersBiso max: 153.47 Å2 / Biso mean: 33.38 Å2 / Biso min: 4.49 Å2
Baniso -1Baniso -2Baniso -3
1-4.974 Å2-0 Å2-7.1914 Å2
2--5.5582 Å20 Å2
3---10.3332 Å2
Refinement stepCycle: LAST / Resolution: 2.454→41.769 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7114 1381 0 255 8750
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088862
X-RAY DIFFRACTIONf_angle_d2.01312382
X-RAY DIFFRACTIONf_chiral_restr0.0711503
X-RAY DIFFRACTIONf_plane_restr0.0091398
X-RAY DIFFRACTIONf_dihedral_angle_d20.7543340
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4539-2.50720.33351340.30052558269299
2.5072-2.56550.31711410.287925982739100
2.5655-2.62970.34841510.301225922743100
2.6297-2.70080.32371410.305426182759100
2.7008-2.78020.34771420.292225922734100
2.7802-2.86990.37851260.290425982724100
2.8699-2.97250.30031450.287125982743100
2.9725-3.09150.32771140.266326372751100
3.0915-3.23210.28051290.239726422771100
3.2321-3.40240.29631310.23426122743100
3.4024-3.61550.24371400.210625902730100
3.6155-3.89450.24161400.189326002740100
3.8945-4.2860.2221580.165126362794100
4.286-4.90540.18331240.16226252749100
4.9054-6.17710.25321520.18932619277199
6.1771-41.7750.19371500.162826732823100
Refinement TLS params.Method: refined / Origin x: -34.3391 Å / Origin y: 14.7695 Å / Origin z: -18.5632 Å
111213212223313233
T0.041 Å20.0311 Å2-0.0125 Å2-0.0038 Å20.0002 Å2--0.0472 Å2
L0.1949 °20.0648 °20.025 °2-0.1736 °20.115 °2--0.1637 °2
S0.0506 Å °-0.0009 Å °0.0054 Å °0.0078 Å °0.0175 Å °0.0226 Å °-0.0273 Å °-0.0004 Å °-0.0153 Å °
Refinement TLS groupSelection details: ALL

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