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- PDB-4bjn: Crystal structure of the flax-rust effector AvrM-A -

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Basic information

Entry
Database: PDB / ID: 4bjn
TitleCrystal structure of the flax-rust effector AvrM-A
ComponentsAVRM-A
KeywordsPROTEIN TRANSPORT / FUNGAL PROTEINS / PLANT DISEASES / IMMUNITY / INNATE / MEMBRANE TRANSLOCATION / PHOSPHATIDYLINOSITOL / STRUCTURE-ACTIVITY RELATIONSHIP VIRULENCE FACTORS
Function / homologyMethane Monooxygenase Hydroxylase; Chain G, domain 1 - #1680 / Flax-rust effector AvrM-A / Flax-rust effector AvrM, N-terminal domain / Flax-rust effector AvrM-A / Flax-rust effector AvrM N-terminal domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha / AvrM-A
Function and homology information
Biological speciesMELAMPSORA LINI (flax rust)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsVe, T. / Williams, S.J. / Kobe, B.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structures of the Flax-Rust Effector Avrm Reveal Insights Into the Molecular Basis of Plant-Cell Entry and Effector-Triggered Immunity
Authors: Ve, T. / Williams, S.J. / Catanzariti, A.M. / Rafiqi, M. / Rahman, M. / Ellis, J.G. / Hardham, A.R. / Jones, D.A. / Anderson, P.A. / Dodds, P.N. / Kobe, B.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Crystallization and X-Ray Diffraction Analysis of the C-Terminal Domain of the Flax Rust Effector Protein Avrm.
Authors: Ve, T. / Williams, S.J. / Stamp, A. / Valkov, E. / Dodds, P.N. / Anderson, P.A. / Kobe, B.
History
DepositionApr 19, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2013Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AVRM-A
B: AVRM-A
C: AVRM-A
D: AVRM-A
E: AVRM-A
F: AVRM-A
G: AVRM-A
H: AVRM-A


Theoretical massNumber of molelcules
Total (without water)223,9288
Polymers223,9288
Non-polymers00
Water0
1
A: AVRM-A
B: AVRM-A


Theoretical massNumber of molelcules
Total (without water)55,9822
Polymers55,9822
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-20 kcal/mol
Surface area24700 Å2
MethodPISA
2
C: AVRM-A

D: AVRM-A


Theoretical massNumber of molelcules
Total (without water)55,9822
Polymers55,9822
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_545x+1/2,y-1/2,z1
Buried area3720 Å2
ΔGint-16.6 kcal/mol
Surface area23480 Å2
MethodPISA
3
D: AVRM-A

C: AVRM-A


Theoretical massNumber of molelcules
Total (without water)55,9822
Polymers55,9822
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_455x-1/2,y+1/2,z1
Buried area3720 Å2
ΔGint-16.6 kcal/mol
Surface area23480 Å2
MethodPISA
4
E: AVRM-A
H: AVRM-A


Theoretical massNumber of molelcules
Total (without water)55,9822
Polymers55,9822
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-20.7 kcal/mol
Surface area24360 Å2
MethodPISA
5
F: AVRM-A

G: AVRM-A


Theoretical massNumber of molelcules
Total (without water)55,9822
Polymers55,9822
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_455x-1/2,y+1/2,z1
Buried area3750 Å2
ΔGint-15.3 kcal/mol
Surface area25210 Å2
MethodPISA
6
G: AVRM-A

F: AVRM-A


Theoretical massNumber of molelcules
Total (without water)55,9822
Polymers55,9822
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_545x+1/2,y-1/2,z1
Buried area3750 Å2
ΔGint-15.3 kcal/mol
Surface area25210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.990, 131.390, 280.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
AVRM-A


Mass: 27991.004 Da / Num. of mol.: 8 / Fragment: RESIDUES 103-343
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MELAMPSORA LINI (flax rust) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q2MV52

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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: 2.4 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growDetails: 50 MM BIS-TRIS PH 6.5, 50 MM AMMONIUM SULFATE, 30% PENTA-ERYTHRITOL ETHOXYLATE (15/4 EO/OH)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.978508
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978508 Å / Relative weight: 1
ReflectionResolution: 2.9→65.7 Å / Num. obs: 48260 / % possible obs: 100 % / Observed criterion σ(I): 1.6 / Redundancy: 14.3 % / Biso Wilson estimate: 89.15 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.3
Reflection shellResolution: 2.9→3 Å / Redundancy: 14.7 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.6 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.9→49.59 Å / Cor.coef. Fo:Fc: 0.9427 / Cor.coef. Fo:Fc free: 0.9242 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.375
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2489 2438 5.06 %RANDOM
Rwork0.2073 ---
obs0.2094 48190 99.87 %-
Displacement parametersBiso mean: 96.28 Å2
Baniso -1Baniso -2Baniso -3
1--5.1901 Å20 Å20 Å2
2---7.05 Å20 Å2
3---12.2401 Å2
Refine analyzeLuzzati coordinate error obs: 0.565 Å
Refinement stepCycle: LAST / Resolution: 2.9→49.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13996 0 0 0 13996
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00914165HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9818981HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d7086SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes437HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1968HARMONIC5
X-RAY DIFFRACTIONt_it14165HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.06
X-RAY DIFFRACTIONt_other_torsion3.19
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1858SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact16174SEMIHARMONIC4
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2843 198 5.61 %
Rwork0.2622 3330 -
all0.2635 3528 -
obs--99.87 %
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)
10.9069-0.1376-0.05331.87710.10662.4794-0.1273-0.481-0.03620.54080.01710.4885-0.5442-0.53780.11020.20.1520.051-0.1701-0.0248-0.30435.307457.6106324.203
21.7304-0.17941.12442.53540.50353.76630.27740.3588-0.3005-0.5442-0.1937-0.09580.52470.4935-0.08360.12230.152-0.0064-0.2859-0.0262-0.302941.194845.2095294.942
31.621-1.20880.74341.2861-1.26473.065-0.1776-0.296-0.08510.33950.29980.3155-0.5059-0.3694-0.1222-0.15510.05540.0063-0.18630.0444-0.056748.192915.1198330.733
43.0321-2.16161.39942.735-2.03882.442-0.0929-0.2033-0.5442-0.10210.28630.54420.5442-0.0293-0.1933-0.07350.0317-0.0749-0.3040.0550.01130.364750.9808331.474
51.72480.06010.58121.23440.25693.73450.1823-0.1665-0.0090.35080.0451-0.1811-0.17080.1905-0.2274-0.1288-0.03090.0173-0.1578-0.0293-0.1687-37.830221.2179336.58
62.6386-1.4675-0.04011.9780.12181.230.298-0.1078-0.0151-0.2516-0.0696-0.54420.19240.3785-0.2284-0.3040.0032-0.0016-0.0403-0.03830.0801-37.189263.9537300.666
71.4171-0.1782-0.60871.43090.27411.99230.20880.31730.3441-0.1465-0.1013-0.0242-0.1963-0.0428-0.1075-0.24710.0260.0004-0.01560.0635-0.0888-8.438611.3687300.429
80.72220.17860.2562.97181.33843.81710.20690.30780.3913-0.5442-0.3350.3001-0.5442-0.54420.1281-0.1820.1520.022-0.0730.037-0.2563-48.174328.7235307.501
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E
6X-RAY DIFFRACTION6CHAIN F
7X-RAY DIFFRACTION7CHAIN G
8X-RAY DIFFRACTION8CHAIN H

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