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- PDB-4osi: Crystal structure of the TAL effector dHax3 with NI RVD at 2.8 an... -

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Basic information

Entry
Database: PDB / ID: 4osi
TitleCrystal structure of the TAL effector dHax3 with NI RVD at 2.8 angstrom resolution
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 / homologyTAL effector repeat / TAL effector repeat / DNA / DNA (> 10) / Hax3
Function and homology information
Biological speciesXanthomonas campestris pv. armoraciae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.849 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)124,3876
Polymers124,3876
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)62,1933
Polymers62,1933
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-57 kcal/mol
Surface area23250 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)62,1933
Polymers62,1933
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-59 kcal/mol
Surface area24100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.289, 89.364, 90.274
Angle α, β, γ (deg.)90.00, 103.74, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hax3


Mass: 51780.586 Da / Num. of mol.: 2 / Fragment: UNP residues 231-720
Mutation: N300H,I301D,N368H,I369D,H402N,D403G,H436N,D437G,H470N,D471G,S505I,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: 2.66 Å3/Da / Density % sol: 53.67 %
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: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. all: 32103 / Num. obs: 30448 / % possible obs: 94.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 75.59 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: 2.849→31.986 Å / FOM work R set: 0.7055 / SU ML: 0.88 / σ(F): 1.34 / Phase error: 35.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2864 1532 5.03 %
Rwork0.2428 28916 -
obs0.2452 30448 99.42 %
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.295 Å2 / ksol: 0.252 e/Å3
Displacement parametersBiso max: 222.14 Å2 / Biso mean: 87.53 Å2 / Biso min: 42.34 Å2
Baniso -1Baniso -2Baniso -3
1--10.9287 Å20 Å2-4.0483 Å2
2---0.9321 Å2-0 Å2
3---16.9609 Å2
Refinement stepCycle: LAST / Resolution: 2.849→31.986 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7024 1342 0 39 8405
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098632
X-RAY DIFFRACTIONf_angle_d1.41112047
X-RAY DIFFRACTIONf_chiral_restr0.0721474
X-RAY DIFFRACTIONf_plane_restr0.0081355
X-RAY DIFFRACTIONf_dihedral_angle_d23.8173253
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8486-2.94050.53071490.3892508265796
2.9405-3.04550.37371280.354426382766100
3.0455-3.16730.3921210.30826612782100
3.1673-3.31130.41291360.316526022738100
3.3113-3.48570.38771470.30926432790100
3.4857-3.70380.33981490.266126172766100
3.7038-3.98930.24361380.223526452783100
3.9893-4.38980.24231320.206926432775100
4.3898-5.02290.22351310.199926522783100
5.0229-6.32040.35271400.261226692809100
6.3204-31.98810.22061610.20112638279998
Refinement TLS params.Method: refined / Origin x: -14.8927 Å / Origin y: -36.1106 Å / Origin z: -25.8037 Å
111213212223313233
T0.5126 Å20.0054 Å20.0093 Å2-0.5679 Å20.0449 Å2--0.6046 Å2
L0.1959 °20.1365 °20.1152 °2-0.3879 °20.3946 °2--0.5269 °2
S0.0396 Å °0.1124 Å °-0.0296 Å °-0.0051 Å °0.0948 Å °-0.2091 Å °0.0111 Å °0.1308 Å °-0.1256 Å °
Refinement TLS groupSelection details: ALL

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