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- PDB-4osz: Crystal structure of the S505P mutant of TAL effector dHax3 -

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Basic information

Entry
Database: PDB / ID: 4osz
TitleCrystal structure of the S505P 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: 2.614 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)124,3556
Polymers124,3556
Non-polymers00
Water2,054114
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)62,1773
Polymers62,1773
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-64 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)62,1773
Polymers62,1773
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-58 kcal/mol
Surface area24070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.312, 86.276, 86.210
Angle α, β, γ (deg.)90.00, 102.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hax3


Mass: 51764.543 Da / Num. of mol.: 2 / Fragment: UNP residues 231-720
Mutation: N300H,I301D,N368H,I369D,H402N,D403G,H436N,D437G,H470N,D471G,S505P,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.: 114 / 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: 48.21 %
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: 2.6→44.8 Å / Num. all: 35168 / Num. obs: 35135 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 43.77 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: 2.614→42.096 Å / FOM work R set: 0.7444 / SU ML: 0.44 / σ(F): 1.34 / Phase error: 31.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2745 1760 5.01 %
Rwork0.2174 33375 -
obs0.2203 35135 99.37 %
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 19.987 Å2 / ksol: 0.294 e/Å3
Displacement parametersBiso max: 131.94 Å2 / Biso mean: 46.19 Å2 / Biso min: 14.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.0397 Å2-0 Å2-15.0648 Å2
2--0.9484 Å20 Å2
3---11.4617 Å2
Refinement stepCycle: LAST / Resolution: 2.614→42.096 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7076 1381 0 114 8571
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088799
X-RAY DIFFRACTIONf_angle_d1.47512296
X-RAY DIFFRACTIONf_chiral_restr0.0771496
X-RAY DIFFRACTIONf_plane_restr0.0071387
X-RAY DIFFRACTIONf_dihedral_angle_d20.9883320
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6144-2.68510.44161190.33142378249793
2.6851-2.76410.37191470.321925642711100
2.7641-2.85330.34341240.300125532677100
2.8533-2.95520.36771290.298525812710100
2.9552-3.07350.3191390.272625742713100
3.0735-3.21330.35141290.246825862715100
3.2133-3.38270.30861450.255225712716100
3.3827-3.59450.29591180.217726022720100
3.5945-3.87190.24821570.19425472704100
3.8719-4.26120.2251280.172325942722100
4.2612-4.8770.22171390.173225792718100
4.877-6.14140.25481420.212126062748100
6.1414-42.1010.22341440.17372640278499
Refinement TLS params.Method: refined / Origin x: -34.7771 Å / Origin y: 13.2714 Å / Origin z: -18.4949 Å
111213212223313233
T0.1668 Å20.0227 Å20.0106 Å2-0.1355 Å20.0163 Å2--0.2027 Å2
L0.611 °20.2196 °20.342 °2-0.3841 °20.2591 °2--0.4738 °2
S0.0029 Å °-0.01 Å °-0.0053 Å °-0.0323 Å °-0.0065 Å °0.0752 Å °-0.0498 Å °-0.0375 Å °-0.0005 Å °
Refinement TLS groupSelection details: ALL

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