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- PDB-2ypf: Structure of the AvrBs3-DNA complex provides new insights into th... -

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Basic information

Entry
Database: PDB / ID: 2ypf
TitleStructure of the AvrBs3-DNA complex provides new insights into the initial thymine-recognition mechanism
Components
  • 5'-D(*TP*AP*GP*AP*GP*GP*GP*TP*TP*AP*GP*GP*TP*TP *TP*AP*TP*AP*TP*AP*AP)-3'
  • 5'-D(*TP*TP*TP*AP*TP*AP*TP*AP*AP*AP*CP*CP*TP*AP *AP*CP*CP*CP*TP*CP*TP*AP)-3'
  • AVRBS3
KeywordsDNA BINDING PROTEIN/DNA / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology: / TAL effector repeat / TAL effector repeat / host cell nucleus / extracellular region / DNA / DNA (> 10) / Hax2
Function and homology information
Biological speciesXANTHOMONAS CAMPESTRIS (bacteria)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsStella, S. / Molina, R. / Yefimenko, I. / Prieto, J. / Silva, G.H. / Bertonati, C. / Juillerat, A. / Duchateau, P. / Montoya, G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structure of the Avrbs3-DNA Complex Provides New Insights Into the Initial Thymine-Recognition Mechanism
Authors: Stella, S. / Molina, R. / Yefimenko, I. / Prieto, J. / Silva, G.H. / Bertonati, C. / Juillerat, A. / Duchateau, P. / Montoya, G.
History
DepositionOct 30, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references / Source and taxonomy / Structure summary
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AVRBS3
B: 5'-D(*TP*TP*TP*AP*TP*AP*TP*AP*AP*AP*CP*CP*TP*AP *AP*CP*CP*CP*TP*CP*TP*AP)-3'
C: 5'-D(*TP*AP*GP*AP*GP*GP*GP*TP*TP*AP*GP*GP*TP*TP *TP*AP*TP*AP*TP*AP*AP)-3'


Theoretical massNumber of molelcules
Total (without water)91,8393
Polymers91,8393
Non-polymers00
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7130 Å2
ΔGint-69.3 kcal/mol
Surface area33500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.110, 100.250, 61.370
Angle α, β, γ (deg.)90.00, 102.55, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein AVRBS3 / AVIRULENCE PROTEIN AVRBS3


Mass: 78653.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) XANTHOMONAS CAMPESTRIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q3ZD73*PLUS
#2: DNA chain 5'-D(*TP*TP*TP*AP*TP*AP*TP*AP*AP*AP*CP*CP*TP*AP *AP*CP*CP*CP*TP*CP*TP*AP)-3'


Mass: 6629.330 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain 5'-D(*TP*AP*GP*AP*GP*GP*GP*TP*TP*AP*GP*GP*TP*TP *TP*AP*TP*AP*TP*AP*AP)-3'


Mass: 6556.268 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growDetails: 0.1M MES PH=6.5, 5-15% PEG3350, 5-15% 2-PROPANOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→32.29 Å / Num. obs: 25764 / % possible obs: 93 % / Observed criterion σ(I): 1.3 / Redundancy: 2.2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 11.79
Reflection shellResolution: 2.55→2.62 Å / Redundancy: 2.07 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1.31 / % possible all: 95.1

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3V6T

3v6t


Resolution: 2.55→32.29 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.918 / SU B: 25.211 / SU ML: 0.284 / Cross valid method: THROUGHOUT / ESU R: 0.97 / ESU R Free: 0.367 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.28983 1373 5.1 %RANDOM
Rwork0.23578 ---
obs0.23857 25764 93.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.161 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20 Å2-0.08 Å2
2---1.27 Å20 Å2
3---0.51 Å2
Refinement stepCycle: LAST / Resolution: 2.55→32.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4772 875 0 175 5822
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0185816
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8971.8298126
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5885674
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.08426.727165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.73715758
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6161515
X-RAY DIFFRACTIONr_chiral_restr0.1120.2973
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214021
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.553→2.619 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 100 -
Rwork0.284 1896 -
obs--93.97 %

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