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- PDB-1ukf: Crystal Structure of Pseudomonas Avirulence Protein AvrPphB -

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Basic information

Entry
Database: PDB / ID: 1ukf
TitleCrystal Structure of Pseudomonas Avirulence Protein AvrPphB
ComponentsAvirulence protein AVRPPH3
KeywordsHYDROLASE / AvrPphB / AvrPph3 / Avirulence / Hypersensitive Response
Function / homology
Function and homology information


symbiont-mediated perturbation of host defense-related programmed cell death / host cell membrane / : / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / cysteine-type endopeptidase activity / extracellular region / membrane
Similarity search - Function
Cathepsin B; Chain A - #20 / Peptidase C58, YopT-type domain / Yersinia/Haemophilus virulence surface antigen / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Cysteine protease avirulence protein AvrPphB
Similarity search - Component
Biological speciesPseudomonas syringae pv. phaseolicola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.35 Å
AuthorsZhu, M. / Shao, F. / Innes, R.W. / Dixon, J.E. / Xu, Z.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2004
Title: The crystal structure of Pseudomonas avirulence protein AvrPphB: a papain-like fold with a distinct substrate-binding site.
Authors: Zhu, M. / Shao, F. / Innes, R.W. / Dixon, J.E. / Xu, Z.
History
DepositionAug 21, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: 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: Avirulence protein AVRPPH3


Theoretical massNumber of molelcules
Total (without water)20,3871
Polymers20,3871
Non-polymers00
Water3,549197
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.601, 49.596, 75.705
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 Avirulence protein AVRPPH3 / Pseudomonas AvrPphB


Mass: 20387.289 Da / Num. of mol.: 1 / Fragment: residues 81-267
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. phaseolicola (bacteria)
Species: Pseudomonas savastanoi / Plasmid: pET21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q52430
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 1.82 Å3/Da / Density % sol: 31.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: Ammonium Sulfate, PIPES, pH 6.7, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris-HCl1droppH7.5
210 mM1dropNaCl
31 mMTCEP-HCl1drop
417 mg/mlprotein1drop
51.95 Mammonium sulfate1reservoir
6100 mMPIPES1reservoirpH6.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792, 0.9879, 0.9793, 0.9565
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jul 4, 2002
RadiationMonochromator: Silicon / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.98791
30.97931
40.95651
ReflectionResolution: 1.3→30.09 Å / Num. all: 41298 / Num. obs: 39746 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 13.3 Å2
Reflection shellResolution: 1.3→1.35 Å / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 2 / Rsym value: 0.035 / % possible all: 75.9
Reflection
*PLUS
Highest resolution: 1.35 Å / Num. measured all: 236773 / Rmerge(I) obs: 0.036
Reflection shell
*PLUS
% possible obs: 93.1 % / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 5

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.35→30.09 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1053609.62 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.222 3553 10 %RANDOM
Rwork0.204 ---
obs0.204 35498 96.4 %-
all-36823 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.0291 Å2 / ksol: 0.423291 e/Å3
Displacement parametersBiso mean: 17.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.03 Å20 Å20 Å2
2---0.84 Å20 Å2
3----0.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.07 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.35→30.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1408 0 0 197 1605
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.35→1.43 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.238 552 10.2 %
Rwork0.228 4876 -
obs--89.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rfree: 0.22 / Rfactor Rwork: 0.203
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.71

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