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- PDB-4oss: Crystal structure of the S505Q mutant of TAL effector dHax3 -

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Basic information

Entry
Database: PDB / ID: 4oss
TitleCrystal structure of the S505Q mutant of TAL effector dHax3
Components
  • DNA (5'-D(*AP*GP*AP*GP*AP*GP*AP*CP*AP*AP*AP*GP*GP*GP*AP*CP*A)-3')
  • DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*TP*GP*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: 2.397 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*GP*TP*CP*TP*CP*TP*CP*T)-3')
H: DNA (5'-D(*AP*GP*AP*GP*AP*GP*AP*CP*AP*AP*AP*GP*GP*GP*AP*CP*A)-3')
I: DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*TP*GP*TP*CP*TP*CP*TP*CP*T)-3')
J: DNA (5'-D(*AP*GP*AP*GP*AP*GP*AP*CP*AP*AP*AP*GP*GP*GP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)124,4196
Polymers124,4196
Non-polymers00
Water1,928107
1
A: Hax3
I: DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*TP*GP*TP*CP*TP*CP*TP*CP*T)-3')
J: DNA (5'-D(*AP*GP*AP*GP*AP*GP*AP*CP*AP*AP*AP*GP*GP*GP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)62,2093
Polymers62,2093
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-67 kcal/mol
Surface area23850 Å2
MethodPISA
2
B: Hax3
G: DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*TP*GP*TP*CP*TP*CP*TP*CP*T)-3')
H: DNA (5'-D(*AP*GP*AP*GP*AP*GP*AP*CP*AP*AP*AP*GP*GP*GP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)62,2093
Polymers62,2093
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-61 kcal/mol
Surface area24330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.083, 87.072, 87.950
Angle α, β, γ (deg.)90.00, 103.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hax3


Mass: 51795.559 Da / Num. of mol.: 2 / Fragment: UNP residues 231-720
Mutation: N300H,I301D,N368H,I369D,H402N,D403G,H436N,D437G,H470N,D471G,S505Q,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*GP*TP*CP*TP*CP*TP*CP*T)-3')


Mass: 5086.280 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*AP*GP*AP*GP*AP*GP*AP*CP*AP*AP*AP*GP*GP*GP*AP*CP*A)-3')


Mass: 5327.502 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.43 Å3/Da / Density % sol: 49.41 %
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: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.397→40 Å / Num. all: 46781 / Num. obs: 46754 / % 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: 2.397→39.503 Å / FOM work R set: 0.7845 / SU ML: 0.33 / σ(F): 1.34 / Phase error: 28.46 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2545 2369 5.07 %
Rwork0.2189 44385 -
obs0.2207 46754 99.54 %
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.138 Å2 / ksol: 0.327 e/Å3
Displacement parametersBiso max: 122.11 Å2 / Biso mean: 47.79 Å2 / Biso min: 24.11 Å2
Baniso -1Baniso -2Baniso -3
1--0.1416 Å2-0 Å2-12.4973 Å2
2---0.9255 Å20 Å2
3---1.7449 Å2
Refinement stepCycle: LAST / Resolution: 2.397→39.503 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7094 1344 0 107 8545
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078819
X-RAY DIFFRACTIONf_angle_d1.24212311
X-RAY DIFFRACTIONf_chiral_restr0.071495
X-RAY DIFFRACTIONf_plane_restr0.0061394
X-RAY DIFFRACTIONf_dihedral_angle_d20.023319
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3965-2.44540.33131230.29332450257394
2.4454-2.49860.35511470.298525832730100
2.4986-2.55670.36651230.287126342757100
2.5567-2.62060.35341370.291425862723100
2.6206-2.69150.32741170.28726542771100
2.6915-2.77060.35111320.278926062738100
2.7706-2.860.29711310.27925802711100
2.86-2.96220.31251660.278226242790100
2.9622-3.08080.30091340.263526232757100
3.0808-3.22090.2861440.250726232767100
3.2209-3.39070.29441450.24226102755100
3.3907-3.6030.2461500.210825992749100
3.603-3.88090.2221450.187726092754100
3.8809-4.27110.19941340.175926672801100
4.2711-4.88810.21531590.168825912750100
4.8881-6.15480.25231210.211426662787100
6.1548-39.50820.19311610.170726802841100
Refinement TLS params.Method: refined / Origin x: -34.3541 Å / Origin y: 14.7108 Å / Origin z: -18.4355 Å
111213212223313233
T0.2751 Å20.0225 Å2-0.0014 Å2-0.2563 Å20.0078 Å2--0.2852 Å2
L0.368 °20.1162 °20.2415 °2-0.1943 °20.1561 °2--0.429 °2
S0.0233 Å °-0.0354 Å °0.0117 Å °0.0027 Å °0.0122 Å °0.0214 Å °-0.0314 Å °-0.0488 Å °-0.034 Å °
Refinement TLS groupSelection details: ALL

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