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- PDB-5fid: Crystal structure of the protein elicitor MoHrip2 from Magnaporth... -

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Basic information

Entry
Database: PDB / ID: 5fid
TitleCrystal structure of the protein elicitor MoHrip2 from Magnaporthe oryzae
ComponentsElicitor protein Hrip2
KeywordsTOXIN / Protein elicitor
Function / homologyBlastomyces yeast-phase-specific protein / Blastomyces yeast-phase-specific protein / Elicitor protein Hrip2
Function and homology information
Biological speciesMagnaporthe oryzae (rice blast fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.809 Å
AuthorsLiu, M. / Duan, L. / Qiu, D. / Liu, X.
Funding support China, 2items
OrganizationGrant numberCountry
National High Technology Research and Development Program of China (863 Program)No.2011AA10A205 China
National Natural Science Foundation of ChiniaNo.31371984 China
CitationJournal: Front Plant Sci / Year: 2016
Title: Crystal Structure Analysis and the Identification of Distinctive Functional Regions of the Protein Elicitor Mohrip2
Authors: Liu, M. / Duan, L. / Wang, M. / Zeng, H. / Liu, X. / Qiu, D.
History
DepositionDec 23, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 7, 2016Provider: 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 / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Elicitor protein Hrip2
B: Elicitor protein Hrip2


Theoretical massNumber of molelcules
Total (without water)29,8562
Polymers29,8562
Non-polymers00
Water7,242402
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-10 kcal/mol
Surface area11330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.245, 43.511, 74.001
Angle α, β, γ (deg.)90.00, 92.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Elicitor protein Hrip2


Mass: 14928.171 Da / Num. of mol.: 2 / Fragment: UNP residues 19-152 / Mutation: L78M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnaporthe oryzae (rice blast fungus) / Gene: hrip2 / Plasmid: pET-30 / Details (production host): modifie / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Codon Plus / References: UniProt: I3RTU7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / 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

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Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.2M ammonium sulfate / PH range: 7.0-9.o

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 1W2B / Wavelength: 0.9792 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.8→31.9 Å / Num. obs: 21184 / % possible obs: 96.6 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 16.8
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.288 / Mean I/σ(I) obs: 2.3 / % possible all: 86.4

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
SCALEPACKdata reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.809→31.883 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2 1042 5.18 %
Rwork0.163 --
obs0.1649 20117 94.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.809→31.883 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2050 0 0 402 2452
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072110
X-RAY DIFFRACTIONf_angle_d1.1512864
X-RAY DIFFRACTIONf_dihedral_angle_d14.181754
X-RAY DIFFRACTIONf_chiral_restr0.084306
X-RAY DIFFRACTIONf_plane_restr0.005380
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8087-1.90410.27931400.2212355X-RAY DIFFRACTION83
1.9041-2.02330.23361350.17012750X-RAY DIFFRACTION96
2.0233-2.17950.23271440.16382706X-RAY DIFFRACTION95
2.1795-2.39880.18311400.16852734X-RAY DIFFRACTION95
2.3988-2.74570.19651490.17872768X-RAY DIFFRACTION96
2.7457-3.45870.19421690.1542828X-RAY DIFFRACTION98
3.4587-31.88780.17681650.14762934X-RAY DIFFRACTION99

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