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- PDB-2nun: The structure of the type III effector AvrB complexed with ADP -

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Basic information

Entry
Database: PDB / ID: 2nun
TitleThe structure of the type III effector AvrB complexed with ADP
ComponentsAvirulence B protein
KeywordsTOXIN/PROTEIN BINDING / type III effector / AvrB / nuclotide / pocket / ADP / TOXIN-PROTEIN BINDING COMPLEX
Function / homology
Function and homology information


extracellular region
Similarity search - Function
Fic-like fold - #20 / Avirulence B/C / Avirulence B/C superfamily / : / Avirulence protein / Fic-like fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Avirulence protein B
Similarity search - Component
Biological speciesPseudomonas syringae pv. glycinea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSinger, A.U. / Desveaux, D. / Wu, A.J. / McNulty, B. / Dangl, J.L. / Sondek, J.
CitationJournal: Plos Pathog. / Year: 2007
Title: Type III Effector Activation via Nucleotide Binding, Phosphorylation, and Host Target Interaction.
Authors: Desveaux, D. / Singer, A.U. / Wu, A.J. / McNulty, B.C. / Musselwhite, L. / Nimchuk, Z. / Sondek, J. / Dangl, J.L.
History
DepositionNov 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Avirulence B protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7313
Polymers36,1811
Non-polymers5492
Water1,54986
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.717, 122.717, 64.091
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Detailsonly one molecule in the asymmetric unit and the biological assembly

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Components

#1: Protein Avirulence B protein


Mass: 36181.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. glycinea (bacteria)
Species: Pseudomonas savastanoi / Strain: pv glycinea / Gene: avrB / Plasmid: pProEX-HTa / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta / References: UniProt: P13835
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 3.85 Å3/Da / Density % sol: 68.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: Protein (8-10 mg/ml) was mixed with well solution (100 mM Glycine, pH 9.0, 20-30% PEG 550 MME)at a 1:1 ratio. Microseeding was employed to obtain better crystals. Nucleotides were ...Details: Protein (8-10 mg/ml) was mixed with well solution (100 mM Glycine, pH 9.0, 20-30% PEG 550 MME)at a 1:1 ratio. Microseeding was employed to obtain better crystals. Nucleotides were incorporated by exchanging drop and resevoir solutions with 20 l 27% PEG 500 MME and 100 mM Tris 7.5 plus 5 mM MgCl2, followed by a final exchange of this solution plus 5 mM nucleotide. Nucleotides were soaked for ~ 1 day. , VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 30, 2005 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→20 Å / Num. all: 29955 / Num. obs: 24091 / % possible obs: 80.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.9 % / Biso Wilson estimate: 45.1 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 28
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 2.63 / Num. unique all: 943 / % possible all: 32

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1NH1

1nh1


Resolution: 2.4→20 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1928271.38 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1.5 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 999 4.8 %RANDOM
Rwork0.232 ---
all0.233 21650 --
obs0.232 20678 95.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.5504 Å2 / ksol: 0.30493 e/Å3
Displacement parametersBiso mean: 52.8 Å2
Baniso -1Baniso -2Baniso -3
1-7.69 Å26.67 Å20 Å2
2--7.69 Å20 Å2
3----15.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.34 Å
Luzzati d res low-4 Å
Luzzati sigma a0.3 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2389 0 35 86 2510
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcbond_it1.041.5
X-RAY DIFFRACTIONc_mcangle_it1.892
X-RAY DIFFRACTIONc_scbond_it1.272
X-RAY DIFFRACTIONc_scangle_it2.052.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.279 130 4.7 %
Rwork0.301 2664 -
obs--78 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4adp_xplor_par.txtadp_xplor_top.txt
X-RAY DIFFRACTION5tmn_xplor_par.txttmn_xplor_top.txt

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