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- PDB-3ugm: Structure of TAL effector PthXo1 bound to its DNA target -

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Basic information

Entry
Database: PDB / ID: 3ugm
TitleStructure of TAL effector PthXo1 bound to its DNA target
Components
  • DNA-1
  • DNA-2
  • TAL effector AvrBs3/PthA
KeywordsTRANSCRIPTION/DNA / Tal effector / TRANSCRIPTION-DNA complex / DNA binding protein
Function / homology
Function and homology information


symbiont-mediated perturbation of host programmed cell death / host cell nucleus / DNA binding / extracellular region
Similarity search - Function
: / TAL effector repeat / TAL effector repeat
Similarity search - Domain/homology
DNA / DNA (> 10) / TAL effector protein PthXo1
Similarity search - Component
Biological speciesXanthomonas oryzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsMak, A.N.S. / Bradley, P. / Cernadas, R.A. / Bogdanove, A.J. / Stoddard, B.L.
CitationJournal: Science / Year: 2012
Title: The Crystal Structure of TAL Effector PthXo1 Bound to Its DNA Target.
Authors: Mak, A.N. / Bradley, P. / Cernadas, R.A. / Bogdanove, A.J. / Stoddard, B.L.
History
DepositionNov 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2012Group: Database references
Revision 1.2Feb 22, 2012Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: TAL effector AvrBs3/PthA
B: DNA-1
C: DNA-2


Theoretical massNumber of molelcules
Total (without water)132,2923
Polymers132,2923
Non-polymers00
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9650 Å2
ΔGint-93 kcal/mol
Surface area46280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.578, 248.481, 54.646
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TAL effector AvrBs3/PthA


Mass: 108904.258 Da / Num. of mol.: 1 / Fragment: UNP residues 21-1043
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas oryzae (bacteria) / Strain: PXO99A / Gene: pthXo1, PXO_00227 / Production host: Escherichia coli (E. coli) / References: UniProt: B2SU53
#2: DNA chain DNA-1


Mass: 11527.443 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic DNA
#3: DNA chain DNA-2


Mass: 11860.620 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic DNA
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.45 Å3/Da / Density % sol: 49.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20mM Tris HCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.975 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 1, 2011
RadiationMonochromator: single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 26980 / Num. obs: 25841 / % possible obs: 95.8 %

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASESphasing
CNSrefinement
RefinementResolution: 3→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2937 1308 4.8 %
Rwork0.2664 24417 -
obs-25725 95.3 %
Solvent computationBsol: 84.6854 Å2
Displacement parametersBiso max: 200 Å2 / Biso mean: 85.0875 Å2 / Biso min: 10.15 Å2
Baniso -1Baniso -2Baniso -3
1--6.631 Å20 Å20 Å2
2--5.324 Å20 Å2
3---1.307 Å2
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6085 1552 0 216 7853
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param

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