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- PDB-6fmb: Crystal structure of the BEC1054 RNase-like effector from the fun... -

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Basic information

Entry
Database: PDB / ID: 6fmb
TitleCrystal structure of the BEC1054 RNase-like effector from the fungal pathogen Blumeria graminis
ComponentsCSEP0064 putative effector protein
KeywordsRNA BINDING PROTEIN / Blumeria graminis / effector / CSEP0064/BEC1054 / RIP / Bimolecular Fluorescence Complementation / split YFP / RALPH / RNA-binding protein / RNase structure / fungal pathogen
Function / homologyhost cell / extracellular region / Secreted effector CSEP0064
Function and homology information
Biological speciesBlumeria graminis f. sp. hordei (grass mildew)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsJones, R. / Garnett, J. / Spanu, P.D. / Cota, E.
CitationJournal: Biorxiv / Year: 2018
Title: Crystal structure of the BEC1054 RNase-like effector from the fungal pathogen Blumeria graminis
Authors: Jones, R. / Garnett, J. / Spanu, P.D.
History
DepositionJan 30, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _citation.journal_id_ISSN / _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: CSEP0064 putative effector protein


Theoretical massNumber of molelcules
Total (without water)10,7821
Polymers10,7821
Non-polymers00
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.520, 60.520, 78.280
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-136-

HOH

21A-164-

HOH

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Components

#1: Protein CSEP0064 putative effector protein


Mass: 10781.907 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Blumeria graminis f. sp. hordei (grass mildew)
Gene: BGHDH14_bgh02874 / Production host: Escherichia coli (E. coli) / References: UniProt: N1JJ94
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 1.92 Å3/Da / Density % sol: 35.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: Purified CSEP0064/BEC1054 was dialysed into crystallisation buffer (10 mM Tris, 150 mM NaCl, pH 7.0) and concentrated to 10 mg/ml for crystallisation. Commercially available solution ...Details: Purified CSEP0064/BEC1054 was dialysed into crystallisation buffer (10 mM Tris, 150 mM NaCl, pH 7.0) and concentrated to 10 mg/ml for crystallisation. Commercially available solution conditions for crystallisation (Hampton Research,CA, USA) were screened. The protein was combined with the mother liquor on a 1:1 ratio in 200 nl drops. Crystals obtained in 0.1 M sodium acetate buffer pH 5.0, supplemented with 30% PEG 4000, 0.4 M (NH4)2SO4 were cryoprotected with 30% glycerol and flash frozen for data collection.

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.92, 0.95
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.921
20.951
ReflectionResolution: 1.3→52.51 Å / Num. obs: 21286 / % possible obs: 99.5 % / Redundancy: 6 % / CC1/2: 0.998 / Net I/σ(I): 23.4
Reflection shellResolution: 1.3→1.34 Å / Mean I/σ(I) obs: 5 / Num. unique obs: 1483 / CC1/2: 0.996

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
xia2data reduction
xia2data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.3→52.41 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.469 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.049 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17645 1092 5.1 %RANDOM
Rwork0.14374 ---
obs0.14536 20158 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.399 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å2-0 Å2
2--0.02 Å2-0 Å2
3----0.05 Å2
Refinement stepCycle: 1 / Resolution: 1.3→52.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms744 0 0 86 830
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.019801
X-RAY DIFFRACTIONr_bond_other_d0.0020.02703
X-RAY DIFFRACTIONr_angle_refined_deg1.5681.9131094
X-RAY DIFFRACTIONr_angle_other_deg1.11431614
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6495105
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.99623.17141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.29915115
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.093156
X-RAY DIFFRACTIONr_chiral_restr0.0880.2113
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02952
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02212
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.771.402398
X-RAY DIFFRACTIONr_mcbond_other1.771.401398
X-RAY DIFFRACTIONr_mcangle_it2.2832.097498
X-RAY DIFFRACTIONr_mcangle_other2.292.106499
X-RAY DIFFRACTIONr_scbond_it2.1781.506403
X-RAY DIFFRACTIONr_scbond_other2.1761.513404
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6372.19592
X-RAY DIFFRACTIONr_long_range_B_refined3.51712.588959
X-RAY DIFFRACTIONr_long_range_B_other3.18511.915917
X-RAY DIFFRACTIONr_rigid_bond_restr6.81331503
X-RAY DIFFRACTIONr_sphericity_free23.595517
X-RAY DIFFRACTIONr_sphericity_bonded8.01951558
LS refinement shellResolution: 1.302→1.336 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 92 -
Rwork0.194 1390 -
obs--96.48 %

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