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- PDB-4bjm: Crystal structure of the flax-rust effector avrM -

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Basic information

Entry
Database: PDB / ID: 4bjm
TitleCrystal structure of the flax-rust effector avrM
ComponentsAVRM
KeywordsPROTEIN TRANSPORT / PLANT DISEASES / IMMUNITY / INNATE / PROTEIN MULTIMERIZATION / PROTEIN BINDING / MEMBRANE TRANSLOCATION / 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
Function and homology information
Biological speciesMELAMPSORA LINI (flax rust)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AVRM
B: AVRM
C: AVRM
D: AVRM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,7005
Polymers109,6644
Non-polymers351
Water2,270126
1
A: AVRM
B: AVRM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8683
Polymers54,8322
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-25.3 kcal/mol
Surface area26370 Å2
MethodPISA
2
C: AVRM
D: AVRM


Theoretical massNumber of molelcules
Total (without water)54,8322
Polymers54,8322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-11.2 kcal/mol
Surface area24470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.470, 125.610, 128.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
AVRM


Mass: 27416.035 Da / Num. of mol.: 4 / Fragment: RESIDUES 46-280
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MELAMPSORA LINI (flax rust) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q2MV46
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 3.34 Å3/Da / Density % sol: 63.22 % / Description: NONE
Crystal growDetails: 0.1 M MES PH 6.5, 1.3 M SODIUM CITRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95394
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95394 Å / Relative weight: 1
ReflectionResolution: 2.6→72.93 Å / Num. obs: 44915 / % possible obs: 100 % / Observed criterion σ(I): 1.5 / Redundancy: 7.3 % / Biso Wilson estimate: 79.53 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 13.5
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.5 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BJM

4bjm


Resolution: 2.6→26.14 Å / Cor.coef. Fo:Fc: 0.9429 / Cor.coef. Fo:Fc free: 0.9231 / SU R Cruickshank DPI: 0.366 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.358 / SU Rfree Blow DPI: 0.238 / SU Rfree Cruickshank DPI: 0.243
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2332 2259 5.04 %RANDOM
Rwork0.2093 ---
obs0.2105 44794 99.98 %-
Displacement parametersBiso mean: 98.18 Å2
Baniso -1Baniso -2Baniso -3
1-2.9565 Å20 Å20 Å2
2--4.3113 Å20 Å2
3----7.2679 Å2
Refine analyzeLuzzati coordinate error obs: 0.461 Å
Refinement stepCycle: LAST / Resolution: 2.6→26.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7092 0 1 126 7219
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017176HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.019624HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3583SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes243HARMONIC2
X-RAY DIFFRACTIONt_gen_planes997HARMONIC5
X-RAY DIFFRACTIONt_it7176HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.28
X-RAY DIFFRACTIONt_other_torsion3.05
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion930SEMIHARMONIC5
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_contact7988SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3016 156 4.81 %
Rwork0.2337 3085 -
all0.237 3241 -
obs--99.98 %
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)
10.7160.05630.72020.7901-0.31470.37930.0012-0.3375-0.17460.00510.095-0.07030.03230.135-0.0962-0.26910.00180.02110.02140.03850.067-2.057524.49590.7601
20-0.5007-0.58551.45860.36932.35070.0466-0.12630.1464-0.5442-0.00240.04770.2275-0.1727-0.04420.0912-0.01390.019-0.10950.0259-0.0529-4.02322.3193-31.6832
30.0864-0.4632-0.91013.03672.17371.45610.01760.0204-0.00830.0587-0.29690.08030.2453-0.25450.2793-0.04110.031-0.0987-0.2062-0.1508-0.1209-9.7806-5.6538-28.3784
40.2298-0.28390.01840.48610.0650.15850.03230.00130.0370.2108-0.015-0.02020.16710.0555-0.01730.17730.0538-0.0611-0.0401-0.1291-0.061113.6886-7.8685-8.0389
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

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