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- PDB-2qvt: Structure of Melampsora lini avirulence protein, AvrL567-D -

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Basic information

Entry
Database: PDB / ID: 2qvt
TitleStructure of Melampsora lini avirulence protein, AvrL567-D
ComponentsAvrL567-D
KeywordsUNKNOWN FUNCTION / AvrL567-A / AvrL567-D / plant disease resistance
Function / homologyImmunoglobulin-like - #2510 / Melampsora lini avirulence protein AvrL567 / Melampsora avirulence protein AvrL567 superfamily / Melampsora lini avirulence protein AvrL567-A / Immunoglobulin-like / Sandwich / Mainly Beta / AvrL567-D
Function and homology information
Biological speciesMelampsora lini (flax rust)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsGuncar, G. / Wang, C.I. / Forwood, J.K. / Teh, T. / Catanzariti, A.M. / Lawrence, G. / Schirra, H.J. / Anderson, P.A. / Ellis, J.G. / Dodds, P.N. / Kobe, B.
CitationJournal: Plant Cell / Year: 2007
Title: Crystal structures of flax rust avirulence proteins AvrL567-A and -D reveal details of the structural basis for flax disease resistance specificity.
Authors: Wang, C.I. / Guncar, G. / Forwood, J.K. / Teh, T. / Catanzariti, A.M. / Lawrence, G.J. / Loughlin, F.E. / Mackay, J.P. / Schirra, H.J. / Anderson, P.A. / Ellis, J.G. / Dodds, P.N. / Kobe, B.
History
DepositionAug 8, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 13, 2019Group: Structure summary / Category: struct_keywords / Item: _struct_keywords.text
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AvrL567-D


Theoretical massNumber of molelcules
Total (without water)16,8961
Polymers16,8961
Non-polymers00
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.474, 45.833, 84.154
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 AvrL567-D


Mass: 16896.322 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Melampsora lini (flax rust) / Strain: Bs1 / Plasmid: pHUE / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q1HBK6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES, 1.66 M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 1, 2005
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.26→50 Å / Num. obs: 7619 / % possible obs: 99.7 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 11.9
Reflection shellResolution: 2.26→2.32 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 8.35 / Num. unique all: 7619 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2opc

2opc


Resolution: 2.26→40.26 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.901 / SU B: 5.007 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.259 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2574 345 4.6 %RANDOM
Rwork0.19648 ---
obs0.19919 7198 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.332 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.26→40.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms913 0 0 103 1016
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.021940
X-RAY DIFFRACTIONr_angle_refined_deg1.7021.9131276
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2345112
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.35123.26146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.01715153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.282156
X-RAY DIFFRACTIONr_chiral_restr0.1060.2136
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02724
X-RAY DIFFRACTIONr_nbd_refined0.2640.2410
X-RAY DIFFRACTIONr_nbtor_refined0.3060.2619
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2810.293
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3170.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.28
X-RAY DIFFRACTIONr_mcbond_it1.0971.5578
X-RAY DIFFRACTIONr_mcangle_it1.8732911
X-RAY DIFFRACTIONr_scbond_it2.6573414
X-RAY DIFFRACTIONr_scangle_it4.1294.5365
LS refinement shellResolution: 2.26→2.32 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 20 -
Rwork0.24 519 -
obs--98.36 %

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