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- PDB-5xmz: Verticillium effector PevD1 -

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Basic information

Entry
Database: PDB / ID: 5xmz
TitleVerticillium effector PevD1
ComponentsEffector protein PevD1
KeywordsSIGNALING PROTEIN / Verticillium / effector / PevD1
Function / homology: / Alternaria alternata allergen 1 / Alternaria alternata allergen 1 / Alt a 1 (AA1)-like domain profile. / extracellular region / Effector protein PevD1
Function and homology information
Biological speciesVerticillium dahliae (fungus)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.85 Å
AuthorsLiu, X. / Zhou, R.
CitationJournal: J. Exp. Bot. / Year: 2017
Title: The asparagine-rich protein NRP interacts with the Verticillium effector PevD1 and regulates the subcellular localization of cryptochrome 2
Authors: Zhou, R. / Zhu, T. / Han, L. / Liu, M. / Xu, M. / Liu, Y. / Han, D. / Qiu, D. / Gong, Q. / Liu, X.
History
DepositionMay 17, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Effector protein PevD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3163
Polymers16,2401
Non-polymers762
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-25 kcal/mol
Surface area7020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.000, 79.489, 55.512
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-364-

HOH

21A-390-

HOH

31A-410-

HOH

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Components

#1: Protein Effector protein PevD1 / Hypersensitive response-inducing protein PevD1


Mass: 16240.050 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Verticillium dahliae (fungus) / Production host: Enterobacteria phage L1 (virus) / References: UniProt: G0Y276
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.97 Å3/Da / Density % sol: 37.56 %
Crystal growTemperature: 293 K / Method: batch mode / Details: 0.5M Sodium Formate, Tris pH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: May 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 11198 / % possible obs: 98.4 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.04 / Rsym value: 0.04 / Net I/σ(I): 15.3

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→35.805 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 25.68
RfactorNum. reflection% reflection
Rfree0.2602 533 4.79 %
Rwork0.2017 --
obs0.2044 11133 98.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.85→35.805 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms932 0 2 122 1056
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007954
X-RAY DIFFRACTIONf_angle_d1.2391290
X-RAY DIFFRACTIONf_dihedral_angle_d14.177343
X-RAY DIFFRACTIONf_chiral_restr0.074138
X-RAY DIFFRACTIONf_plane_restr0.004174
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.848-2.0340.25671190.18592614X-RAY DIFFRACTION99
2.034-2.32830.26621350.19772661X-RAY DIFFRACTION100
2.3283-2.93320.28241390.22622659X-RAY DIFFRACTION99
2.9332-35.81150.24721400.19432666X-RAY DIFFRACTION96

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