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- PDB-1nh1: Crystal Structure of the Type III Effector AvrB from Pseudomonas ... -

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Basic information

Entry
Database: PDB / ID: 1nh1
TitleCrystal Structure of the Type III Effector AvrB from Pseudomonas syringae.
ComponentsAvirulence B protein
KeywordsAvirulence Protein / HELIX BUNDLE
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
Avirulence protein B
Similarity search - Component
Biological speciesPseudomonas syringae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsLee, C.C. / Wood, M.D. / Ng, K. / Luginbuhl, P. / Spraggon, G. / Katagiri, F.
CitationJournal: Structure / Year: 2004
Title: Crystal Structure of the Type III Effector AvrB from Pseudomonas syringae.
Authors: Lee, C.C. / Wood, M.D. / Ng, K. / Luginbuhl, P. / Spraggon, G. / Katagiri, F.
History
DepositionDec 18, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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

Downloads & links

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Assembly

Deposited unit
A: Avirulence B protein


Theoretical massNumber of molelcules
Total (without water)37,0971
Polymers37,0971
Non-polymers00
Water2,720151
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.028, 125.028, 63.246
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Avirulence B protein


Mass: 37097.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae (bacteria) / Gene: AVRB / Plasmid: pET-27b(+) / Cell line (production host): BL21 (DE3) pLysS / Production host: Escherichia coli (E. coli) / References: UniProt: P13835
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 68.01 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.9 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris1droppH7.9
250 mM1dropNaCl
30.25 mMTCEP1drop
49.5 mg/mlprotein1drop
540 %PEG6001reservoir
6100 mMCHES1reservoirpH9.5-10.0

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12001
21
Diffraction source
SourceSiteBeamlineTypeID
ROTATING ANODERIGAKU1
SYNCHROTRONALS 5.0.22
Detector
TypeIDDetector
RIGAKU1IMAGE PLATE
MARRESEARCH2IMAGE PLATE
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 29594 / Num. obs: 27892 / % possible obs: 94.2 %
Reflection
*PLUS
Lowest resolution: 50 Å / % possible obs: 93.4 % / Rmerge(I) obs: 0.066
Reflection shell
*PLUS
% possible obs: 64.6 % / Rmerge(I) obs: 0.493

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Processing

SoftwareName: CNS / Classification: refinement
RefinementMethod to determine structure: MAD / Resolution: 2.2→50 Å
RfactorNum. reflection% reflection
Rfree0.2751 1419 -
Rwork0.222 --
all-29594 -
obs-27892 94.2 %
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2249 0 0 151 2400
Refinement
*PLUS
Lowest resolution: 500 Å / Rfactor Rfree: 0.275
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.0104
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.54

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