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

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Basic information

Entry
Database: PDB / ID: 4fpq
TitleStructure of a fungal protein
ComponentsAvirulence Effector AvrLm4-7
KeywordsPROTEIN BINDING / alpha-beta protein / Aviraulence protein
Function / homologyAvirulence Effector AvrLm4-7 / Avirulence Effector AvrLm4-7 / Avirulence Effector AvrLm4-7 domain-containing protein
Function and homology information
Biological speciesLeptosphaeria maculans (blackleg of rapeseed fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBlondeau, K. / Blaise, F. / Graille, M. / Linglin, J. / Ollivier, B. / Labarde, A. / Doizy, A. / Daverdin, G. / Balesdent, MH. / Rouxel, T. ...Blondeau, K. / Blaise, F. / Graille, M. / Linglin, J. / Ollivier, B. / Labarde, A. / Doizy, A. / Daverdin, G. / Balesdent, MH. / 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 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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
Water3,603200
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 area1590 Å2
ΔGint-7 kcal/mol
Surface area14520 Å2
MethodPISA
6
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 area1630 Å2
ΔGint-7 kcal/mol
Surface area14540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.830, 60.830, 155.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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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


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.41 Å3/Da / Density % sol: 48.98 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 8
Details: 1.2M Na/K tartrate, 100 mM Tris pH8, 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
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 4, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
101
297911
ReflectionResolution: 2.3→30 Å / Num. all: 25106 / Num. obs: 24177 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 13.6
Reflection shellResolution: 2.3→2.43 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 3.6 / % possible all: 99.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPmodel building
PHENIX(phenix.refine)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→28.315 Å / SU ML: 0.49 / σ(F): 1.99 / Phase error: 34.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3082 1202 5 %RANDOM
Rwork0.2436 ---
all0.25 24036 --
obs0.2468 24036 96.21 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.613 Å2 / ksol: 0.37 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.0767 Å20 Å2-0 Å2
2--6.0767 Å20 Å2
3----12.1534 Å2
Refinement stepCycle: LAST / Resolution: 2.3→28.315 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4066 0 0 200 4266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084231
X-RAY DIFFRACTIONf_angle_d1.0835729
X-RAY DIFFRACTIONf_dihedral_angle_d16.5341525
X-RAY DIFFRACTIONf_chiral_restr0.074613
X-RAY DIFFRACTIONf_plane_restr0.005739
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.39210.31591370.24972629X-RAY DIFFRACTION100
2.3921-2.50090.34831380.24282616X-RAY DIFFRACTION100
2.5009-2.63270.40271390.26882632X-RAY DIFFRACTION100
2.6327-2.79750.44471230.3242345X-RAY DIFFRACTION89
2.7975-3.01330.37291390.26632635X-RAY DIFFRACTION100
3.0133-3.31610.29991390.24432627X-RAY DIFFRACTION100
3.3161-3.7950.35431230.25492352X-RAY DIFFRACTION89
3.795-4.77750.24551320.20382507X-RAY DIFFRACTION95
4.7775-28.31750.23351320.18572491X-RAY DIFFRACTION93

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