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- PDB-5z1v: Crystal structure of AvrPib -

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Basic information

Entry
Database: PDB / ID: 5z1v
TitleCrystal structure of AvrPib
ComponentsAvrPib protein
KeywordsUNKNOWN FUNCTION / Magnaporthe oryzae / MAX effector / protein crystal structure
Function / homologyAvrPib protein
Function and homology information
Biological speciesMagnaporthe oryzae (rice blast fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.661 Å
AuthorsZhang, X. / He, D. / Zhao, Y.X. / Taylor, I.A. / Peng, Y.L. / Yang, J. / Liu, J.F.
CitationJournal: Plant J. / Year: 2018
Title: A positive-charged patch and stabilized hydrophobic core are essential for avirulence function of AvrPib in the rice blast fungus.
Authors: Zhang, X. / He, D. / Zhao, Y. / Cheng, X. / Zhao, W. / Taylor, I.A. / Yang, J. / Liu, J. / Peng, Y.L.
History
DepositionDec 28, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 16, 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: AvrPib protein
B: AvrPib protein
C: AvrPib protein
D: AvrPib protein


Theoretical massNumber of molelcules
Total (without water)29,7524
Polymers29,7524
Non-polymers00
Water6,143341
1
A: AvrPib protein


Theoretical massNumber of molelcules
Total (without water)7,4381
Polymers7,4381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: AvrPib protein


Theoretical massNumber of molelcules
Total (without water)7,4381
Polymers7,4381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: AvrPib protein


Theoretical massNumber of molelcules
Total (without water)7,4381
Polymers7,4381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: AvrPib protein


Theoretical massNumber of molelcules
Total (without water)7,4381
Polymers7,4381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)28.542, 65.840, 55.634
Angle α, β, γ (deg.)90.00, 93.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
AvrPib protein


Mass: 7437.914 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnaporthe oryzae (rice blast fungus) / Gene: AvrPib / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H4ITX1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 1.76 Å3/Da / Density % sol: 30.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2M sodium thiocyanate pH 6.9, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9776 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9776 Å / Relative weight: 1
ReflectionResolution: 1.66→42.45 Å / Num. obs: 24125 / % possible obs: 99.3 % / Redundancy: 6.5 % / CC1/2: 0.994 / Rmerge(I) obs: 0.131 / Net I/σ(I): 15.7
Reflection shellResolution: 1.66→1.72 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.661→42.449 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.23 / Phase error: 23.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2446 1984 8.23 %
Rwork0.1972 --
obs0.2011 24121 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.661→42.449 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1849 0 0 341 2190
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091893
X-RAY DIFFRACTIONf_angle_d1.122550
X-RAY DIFFRACTIONf_dihedral_angle_d18.1681128
X-RAY DIFFRACTIONf_chiral_restr0.063282
X-RAY DIFFRACTIONf_plane_restr0.005318
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6611-1.70270.37241210.29451539X-RAY DIFFRACTION97
1.7027-1.74870.29811580.26361558X-RAY DIFFRACTION99
1.7487-1.80020.32621360.24791609X-RAY DIFFRACTION99
1.8002-1.85830.26011500.21761516X-RAY DIFFRACTION100
1.8583-1.92470.26811340.21131603X-RAY DIFFRACTION99
1.9247-2.00170.26381420.20791582X-RAY DIFFRACTION99
2.0017-2.09280.25391370.21281576X-RAY DIFFRACTION99
2.0928-2.20320.25051580.2011586X-RAY DIFFRACTION100
2.2032-2.34120.29351410.19481578X-RAY DIFFRACTION100
2.3412-2.52190.26771450.20741566X-RAY DIFFRACTION100
2.5219-2.77570.20711390.20861610X-RAY DIFFRACTION100
2.7757-3.17720.22241400.18141583X-RAY DIFFRACTION99
3.1772-4.00250.20621400.1671607X-RAY DIFFRACTION100
4.0025-42.46280.22051430.1711624X-RAY DIFFRACTION100

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