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- PDB-4osr: Crystal structure of the S505K mutant of TAL effector dHax3 -

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Basic information

Entry
Database: PDB / ID: 4osr
TitleCrystal structure of the S505K 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*GP*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: 1.944 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

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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*TP*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*TP*AP*AP*AP*GP*GP*GP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)124,4516
Polymers124,4516
Non-polymers00
Water12,358686
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*TP*AP*AP*AP*GP*GP*GP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)62,2253
Polymers62,2253
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5750 Å2
ΔGint-65 kcal/mol
Surface area23900 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*TP*AP*AP*AP*GP*GP*GP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)62,2253
Polymers62,2253
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-60 kcal/mol
Surface area24400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.052, 87.370, 88.101
Angle α, β, γ (deg.)90.00, 102.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hax3


Mass: 51796.609 Da / Num. of mol.: 2 / Fragment: UNP residues 231-720
Mutation: N300H,I301D,N368H,I369D,H402N,D403G,H436N,D437G,H470N,D471G,S505K,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*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.: 686 / 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: 2.44 Å3/Da / Density % sol: 49.65 %
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: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.944→40 Å / Num. all: 87844 / Num. obs: 87813 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
DNAdata 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: 1.944→33.172 Å / FOM work R set: 0.8175 / SU ML: 0.22 / σ(F): 1.34 / Phase error: 25.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2344 4400 5.01 %
Rwork0.2003 83413 -
obs0.202 87813 99.62 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.094 Å2 / ksol: 0.339 e/Å3
Displacement parametersBiso max: 117.69 Å2 / Biso mean: 35.21 Å2 / Biso min: 15.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.0446 Å2-0 Å2-8.3559 Å2
2---0.6968 Å20 Å2
3---1.8381 Å2
Refinement stepCycle: LAST / Resolution: 1.944→33.172 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7100 1346 0 686 9132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078812
X-RAY DIFFRACTIONf_angle_d1.25212300
X-RAY DIFFRACTIONf_chiral_restr0.0671493
X-RAY DIFFRACTIONf_plane_restr0.0061390
X-RAY DIFFRACTIONf_dihedral_angle_d19.5773318
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9437-1.96570.28471070.30162496260390
1.9657-1.98890.34611410.298228452986100
1.9889-2.01310.35371230.285927582881100
2.0131-2.03860.30111370.26627992936100
2.0386-2.06540.31121460.268227892935100
2.0654-2.09370.2781360.260927852921100
2.0937-2.12360.32281400.25827712911100
2.1236-2.15530.26791480.246327562904100
2.1553-2.1890.26851460.237628042950100
2.189-2.22490.31121530.230827312884100
2.2249-2.26320.27671630.230628052968100
2.2632-2.30440.2441690.220227522921100
2.3044-2.34870.27221390.213127772916100
2.3487-2.39660.20011480.207728002948100
2.3966-2.44870.25571820.210227652947100
2.4487-2.50560.27991200.200827892909100
2.5056-2.56830.22721540.213527762930100
2.5683-2.63770.23831430.222128112954100
2.6377-2.71530.27161440.218727752919100
2.7153-2.80290.24571450.214427972942100
2.8029-2.9030.28871670.221427762943100
2.903-3.01910.281480.213927762924100
3.0191-3.15650.21591540.208927882942100
3.1565-3.32270.24621290.203428112940100
3.3227-3.53070.23321490.183128152964100
3.5307-3.80290.20541380.170328022940100
3.8029-4.1850.1961740.160827722946100
4.185-4.7890.1821440.158128322976100
4.789-6.02770.24791550.186127972952100
6.0277-33.17650.15881580.16332863302199
Refinement TLS params.Method: refined / Origin x: -3.7448 Å / Origin y: 14.8569 Å / Origin z: 24.3339 Å
111213212223313233
T0.188 Å20.0214 Å20.0164 Å2-0.1577 Å20.0009 Å2--0.1877 Å2
L0.3303 °20.109 °20.2125 °2-0.1173 °20.132 °2--0.3504 °2
S0.0316 Å °0.0264 Å °-0.0105 Å °0.0007 Å °0.0133 Å °-0.0083 Å °0.0026 Å °0.0172 Å °-0.0431 Å °
Refinement TLS groupSelection details: ALL

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