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- PDB-4fpr: Structure of a fungal protein -

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Basic information

Entry
Database: PDB / ID: 4fpr
TitleStructure of a fungal protein
ComponentsAvirulence Effector AvrLm4-7
KeywordsPROTEIN BINDING / Alpha-beta protein / Avirulence protein
Function / homologyAlpha-Beta Plaits - #2910 / Avirulence Effector AvrLm4-7 / Avirulence Effector AvrLm4-7 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / Avirulence Effector AvrLm4-7 domain-containing protein
Function and homology information
Biological speciesLeptosphaeria maculans (blackleg of rapeseed fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.402 Å
AuthorsBlondeau, K. / Blaise, F. / Graille, M. / Linglin, J. / Ollivier, B. / Labarde, A. / Doizy, A. / Daverdin, G. / Balesdent, M.H. / Rouxel, T. ...Blondeau, K. / Blaise, F. / Graille, M. / Linglin, J. / Ollivier, B. / Labarde, A. / Doizy, A. / Daverdin, G. / Balesdent, M.H. / Rouxel, T. / van Tilbeurgh, H. / Fudal, I.
CitationJournal: Plant J. / Year: 2015
Title: Crystal structure of the effector AvrLm4-7 of Leptosphaeria maculans reveals insights into its translocation into plant cells and recognition by resistance proteins.
Authors: Blondeau, K. / Blaise, F. / Graille, M. / Kale, S.D. / Linglin, J. / Ollivier, B. / Labarde, A. / Lazar, N. / Daverdin, G. / Balesdent, M.H. / Choi, D.H. / Tyler, B.M. / Rouxel, T. / van ...Authors: Blondeau, K. / Blaise, F. / Graille, M. / Kale, S.D. / Linglin, J. / Ollivier, B. / Labarde, A. / Lazar, N. / Daverdin, G. / Balesdent, M.H. / Choi, D.H. / Tyler, B.M. / Rouxel, T. / van Tilbeurgh, H. / Fudal, I.
History
DepositionJun 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Aug 3, 2022Group: Database references
Category: citation / citation_author ...citation / citation_author / database_2 / struct_ref_seq_dif
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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 Effector AvrLm4-7
B: Avirulence Effector AvrLm4-7
C: Avirulence Effector AvrLm4-7
D: Avirulence Effector AvrLm4-7


Theoretical massNumber of molelcules
Total (without water)59,5204
Polymers59,5204
Non-polymers00
Water4,684260
1
A: Avirulence Effector AvrLm4-7


Theoretical massNumber of molelcules
Total (without water)14,8801
Polymers14,8801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Avirulence Effector AvrLm4-7


Theoretical massNumber of molelcules
Total (without water)14,8801
Polymers14,8801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Avirulence Effector AvrLm4-7


Theoretical massNumber of molelcules
Total (without water)14,8801
Polymers14,8801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Avirulence Effector AvrLm4-7


Theoretical massNumber of molelcules
Total (without water)14,8801
Polymers14,8801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Avirulence Effector AvrLm4-7
B: Avirulence Effector AvrLm4-7


Theoretical massNumber of molelcules
Total (without water)29,7602
Polymers29,7602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-11 kcal/mol
Surface area14460 Å2
MethodPISA
6


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6650 Å2
ΔGint-31 kcal/mol
Surface area25720 Å2
MethodPISA
7
C: Avirulence Effector AvrLm4-7
D: Avirulence Effector AvrLm4-7


Theoretical massNumber of molelcules
Total (without water)29,7602
Polymers29,7602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-11 kcal/mol
Surface area14430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.150, 61.150, 155.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 5:134 )
211chain C and (resseq 5:134 )
112chain B and (resseq 7:133 )
212chain D and (resseq 7:133 )

NCS ensembles :
ID
1
2

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Components

#1: Protein
Avirulence Effector AvrLm4-7


Mass: 14879.876 Da / Num. of mol.: 4 / Mutation: I80K, G120R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptosphaeria maculans (blackleg of rapeseed fungus)
Strain: JN3 / isolate v23.1.3 / race Av1-4-5-6-7-8 / Gene: AvrLm4-7, LEMA_P086290.1 / Production host: Komagataella pastoris (fungus) / References: UniProt: E5A6Z5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.44 Å3/Da / Density % sol: 49.59 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 7
Details: 1.6M ammonium sulfate, 0.1M Hepes pH7, VAPOR DIFFUSION, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 4, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.4→45 Å / Num. all: 43872 / Num. obs: 43302 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 15
Reflection shellResolution: 2.4→2.46 Å / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 3.3 / % possible all: 98.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.402→33.189 Å / SU ML: 0.45 / σ(F): 1.24 / Phase error: 30.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.283 1130 5.14 %
Rwork0.2085 --
obs0.2121 43266 98.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.918 Å2 / ksol: 0.333 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.6695 Å20 Å2-0 Å2
2--5.6695 Å20 Å2
3----11.339 Å2
Refinement stepCycle: LAST / Resolution: 2.402→33.189 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4076 0 0 260 4336
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084239
X-RAY DIFFRACTIONf_angle_d1.1325739
X-RAY DIFFRACTIONf_dihedral_angle_d17.6971525
X-RAY DIFFRACTIONf_chiral_restr0.084613
X-RAY DIFFRACTIONf_plane_restr0.006742
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1044X-RAY DIFFRACTIONPOSITIONAL
12C1044X-RAY DIFFRACTIONPOSITIONAL0.013
21B1003X-RAY DIFFRACTIONPOSITIONAL
22D1003X-RAY DIFFRACTIONPOSITIONAL0.046
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4023-2.45450.39531180.30892602X-RAY DIFFRACTION98
2.4545-2.51160.35281400.27122535X-RAY DIFFRACTION100
2.5116-2.57440.35231500.26332624X-RAY DIFFRACTION100
2.5744-2.6440.32151220.25052618X-RAY DIFFRACTION99
2.644-2.72170.31171360.23382494X-RAY DIFFRACTION97
2.7217-2.80950.32091750.23072564X-RAY DIFFRACTION100
2.8095-2.90990.31641280.21322660X-RAY DIFFRACTION100
2.9099-3.02630.28381360.20312579X-RAY DIFFRACTION100
3.0263-3.1640.33281610.20212523X-RAY DIFFRACTION100
3.164-3.33060.27661700.22052610X-RAY DIFFRACTION100
3.3306-3.53910.31521410.18432491X-RAY DIFFRACTION97
3.5391-3.8120.25751400.18322544X-RAY DIFFRACTION97
3.812-4.19490.22611370.16422388X-RAY DIFFRACTION93
4.1949-4.80040.21971200.14392613X-RAY DIFFRACTION100
4.8004-6.0420.20421350.162593X-RAY DIFFRACTION100
6.042-33.19250.18371160.17932603X-RAY DIFFRACTION99

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