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- PDB-4hpz: Crystal structure of a TALE protein reveals an extended N-termina... -

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Basic information

Entry
Database: PDB / ID: 4hpz
TitleCrystal structure of a TALE protein reveals an extended N-terminal DNA binding region
ComponentsdTale2
KeywordsDNA BINDING PROTEIN / N-TERMINAL DOMAIN / TAL EFFECTOR
Function / homologyTAL effector repeat / TAL effector repeat / host cell nucleus / extracellular region / dTale2
Function and homology information
Biological speciesXanthomonas (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.202 Å
AuthorsChai, J. / Han, Z. / Gao, H.
CitationJournal: Cell Res. / Year: 2012
Title: Crystal structure of a TALE protein reveals an extended N-terminal DNA binding region
Authors: Gao, H. / Wu, X. / Chai, J. / Han, Z.
History
DepositionOct 25, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references / Structure summary
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: dTale2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5684
Polymers48,2801
Non-polymers2883
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.284, 101.284, 95.592
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-914-

HOH

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Components

#1: Protein dTale2


Mass: 48280.113 Da / Num. of mol.: 1 / Fragment: dTale2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas (bacteria) / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: L7MTL1*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THIS HIGHLY-CONSERVED ...A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THIS HIGHLY-CONSERVED PROTEIN WAS CONSTRUCTED BASED ON AvrBs3.

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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: 2.93 Å3/Da / Density % sol: 58.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.05M MgSO4, 0.05M HEPES, 1.6M Li2SO4, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 27, 2011
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.2→15 Å / Num. all: 29024 / Num. obs: 29024 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10.9 % / Rmerge(I) obs: 0.069
Reflection shellResolution: 2.2→2.24 Å / % possible all: 85.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: dev_596)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V6P

3v6p


Resolution: 2.202→14.975 Å / SU ML: 0.24 / σ(F): 0 / Phase error: 26.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2428 1468 5.07 %RANDOM
Rwork0.206 ---
all0.2079 29024 --
obs0.2079 28963 99.86 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.732 Å2 / ksol: 0.392 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.787 Å2-0 Å2-0 Å2
2--7.787 Å20 Å2
3----15.5741 Å2
Refinement stepCycle: LAST / Resolution: 2.202→14.975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3171 0 15 160 3346
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083235
X-RAY DIFFRACTIONf_angle_d1.1844416
X-RAY DIFFRACTIONf_dihedral_angle_d16.3641173
X-RAY DIFFRACTIONf_chiral_restr0.077537
X-RAY DIFFRACTIONf_plane_restr0.005582
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.202-2.28030.29981310.22782716
2.2803-2.37130.2941500.23122710
2.3713-2.47880.33491660.23682681
2.4788-2.60880.28461580.23652705
2.6088-2.77130.28531480.22882738
2.7713-2.98370.26661490.22362745
2.9837-3.28110.23431460.2312736
3.2811-3.74940.25351400.20382778
3.7494-4.69950.18981330.17022797
4.6995-14.97490.21261470.19162889
Refinement TLS params.Method: refined / Origin x: 17.7169 Å / Origin y: 55.0361 Å / Origin z: -25.2695 Å
111213212223313233
T0.1506 Å20.0798 Å2-0.0368 Å2-0.2138 Å20.0033 Å2--0.2156 Å2
L0.1514 °20.254 °20.0274 °2-0.0643 °20.0561 °2--0.4933 °2
S0.0634 Å °0.0592 Å °-0.0352 Å °-0.0131 Å °-0.037 Å °0.0015 Å °0.0731 Å °0.0537 Å °0 Å °
Refinement TLS groupSelection details: all

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