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- PDB-5vjj: Crystal structure of the flax-rust effector AvrP -

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Basic information

Entry
Database: PDB / ID: 5vjj
TitleCrystal structure of the flax-rust effector AvrP
ComponentsAvirulence protein AvrP123Gene-for-gene relationship
KeywordsMETAL BINDING PROTEIN / flax rust (Melampsora lini) effector / nuclear localisation / plant disease resistance / zinc finger
Function / homologyAvirulence protein AvrP123
Function and homology information
Biological speciesMelampsora lini (flax rust)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.52 Å
AuthorsZhang, X. / Ericsson, D.J. / Williams, S.J. / Kobe, B.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP120100685, DP130104098 and DP160102244 Australia
Citation
Journal: Mol. Plant Pathol. / Year: 2018
Title: Crystal structure of the Melampsora lini effector AvrP reveals insights into a possible nuclear function and recognition by the flax disease resistance protein P.
Authors: Zhang, X. / Farah, N. / Rolston, L. / Ericsson, D.J. / Catanzariti, A.M. / Bernoux, M. / Ve, T. / Bendak, K. / Chen, C. / Mackay, J.P. / Lawrence, G.J. / Hardham, A. / Ellis, J.G. / ...Authors: Zhang, X. / Farah, N. / Rolston, L. / Ericsson, D.J. / Catanzariti, A.M. / Bernoux, M. / Ve, T. / Bendak, K. / Chen, C. / Mackay, J.P. / Lawrence, G.J. / Hardham, A. / Ellis, J.G. / Williams, S.J. / Dodds, P.N. / Jones, D.A. / Kobe, B.
#1: Journal: Mol. Plant Pathol. / Year: 2017
Title: Production of small cysteine-rich effector proteins in Escherichia coli for structural and functional studies.
Authors: Zhang, X. / Nguyen, N. / Breen, S. / Outram, M.A. / Dodds, P.N. / Kobe, B. / Solomon, P.S. / Williams, S.J.
History
DepositionApr 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Avirulence protein AvrP123
B: Avirulence protein AvrP123
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0018
Polymers19,6082
Non-polymers3926
Water0
1
A: Avirulence protein AvrP123
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0004
Polymers9,8041
Non-polymers1963
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Avirulence protein AvrP123
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0004
Polymers9,8041
Non-polymers1963
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.937, 88.937, 45.782
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Avirulence protein AvrP123 / Gene-for-gene relationship


Mass: 9804.060 Da / Num. of mol.: 2 / Fragment: UNP residues 23-111
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Melampsora lini (flax rust) / Production host: Escherichia coli (E. coli) / References: UniProt: B2ZCS6
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn

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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: 2.31 Å3/Da / Density % sol: 46.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M Bis-Tris pH 7.0, 22% (w/v) PEG 3350 and 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 1.282, 1.262
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 3, 2013
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.2821
21.2621
ReflectionResolution: 2.52→37.01 Å / Num. obs: 6602 / % possible obs: 99.8 % / Redundancy: 13.2 % / Rpim(I) all: 0.049 / Rrim(I) all: 0.182 / Net I/σ(I): 16.6
Reflection shellResolution: 2.52→2.65 Å / Mean I/σ(I) obs: 2.5 / Rrim(I) all: 0.891

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Blu-Icedata collection
CRANKphasing
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.52→37.01 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / Phase error: 25.7
RfactorNum. reflection% reflection
Rfree0.2642 555 4.69 %
Rwork0.2215 --
obs0.2235 6594 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.52→37.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1147 0 6 0 1153
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071202
X-RAY DIFFRACTIONf_angle_d0.7611643
X-RAY DIFFRACTIONf_dihedral_angle_d9.539725
X-RAY DIFFRACTIONf_chiral_restr0.048168
X-RAY DIFFRACTIONf_plane_restr0.004224
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5185-2.77180.31091360.25392791X-RAY DIFFRACTION99
2.7718-3.17270.27251380.24192822X-RAY DIFFRACTION100
3.1727-3.99650.27171380.21432831X-RAY DIFFRACTION100
3.9965-37.01680.24041430.20682826X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6631-0.57961.18460.4853-0.84842.53790.07830.67440.66880.3831-0.18680.0537-0.37820.2214-0.02670.3544-0.0020.0390.37150.06520.2616-17.417927.3276-0.6286
23.809-1.3682-2.25561.79310.43011.4601-0.4839-0.6305-0.62210.73750.3531-0.3799-0.0223-0.278-0.22680.3713-0.0357-0.11980.3908-0.09820.3776-0.89329.901713.4329
30.9047-0.487-0.5791.2703-0.07670.40850.01280.1371-0.19470.1116-0.1364-0.06110.1848-0.15340.01760.1774-0.0307-0.01790.1809-0.0140.2372-2.253120.94783.2798
43.93670.2991-0.84129.3061-5.27983.1258-0.52580.03290.00061.14070.1917-0.62470.1120.00980.04130.42020.08530.08370.1786-0.03130.274913.284911.119210.2365
50.9435-0.73130.30162.4948-0.6052-0.23940.0216-0.39690.01450.41870.13970.10990.1383-0.0329-0.06740.30330.0003-0.02330.28970.04050.30685.171318.19127.9638
63.1919-1.62091.96894.4315-1.91963.7456-0.50980.0430.4330.96110.68030.10720.08320.03570.03920.4840.12640.08250.44240.07170.34647.94697.893716.6548
70.49140.3058-0.86482.489-1.60172.538-0.1687-0.7084-0.37930.63850.49590.6603-0.3874-0.4450.80980.25030.0988-0.11490.59920.56160.54629.2539-0.240316.5428
88.3973-5.55880.59723.7761-0.98524.30960.4207-0.48720.4572-0.57220.12120.31-1.3006-0.91690.1160.40710.05940.12350.3399-0.03520.7356-2.943835.742839.7056
91.3367-0.45950.03931.09210.22890.6507-0.18350.2254-0.14920.11290.36320.5212-0.20880.0437-0.01490.2156-0.05780.03480.2918-0.04330.2837.231725.935341.0258
101.5397-1.0792-2.11170.79071.44082.62220.3915-0.21240.184-0.69830.0277-0.091-0.55580.2481-0.11530.408-0.0210.07170.2145-0.02840.286119.652430.376620.5416
111.6723-0.9924-1.5170.59850.6571.12220.04370.2617-0.3162-0.0694-0.20120.1633-0.2557-0.098-0.01340.2593-0.02940.01950.2634-0.06010.275313.105627.278730.337
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 26 through 32 )
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 40 )
3X-RAY DIFFRACTION3chain 'A' and (resid 41 through 53 )
4X-RAY DIFFRACTION4chain 'A' and (resid 54 through 58 )
5X-RAY DIFFRACTION5chain 'A' and (resid 59 through 89 )
6X-RAY DIFFRACTION6chain 'A' and (resid 90 through 96 )
7X-RAY DIFFRACTION7chain 'A' and (resid 97 through 102 )
8X-RAY DIFFRACTION8chain 'B' and (resid 28 through 32 )
9X-RAY DIFFRACTION9chain 'B' and (resid 33 through 58 )
10X-RAY DIFFRACTION10chain 'B' and (resid 59 through 70 )
11X-RAY DIFFRACTION11chain 'B' and (resid 71 through 102 )

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