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- PDB-7yww: Monocot chimeric jacalin JAC1 from Oryza sativa: lectin domain (c... -

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Basic information

Entry
Database: PDB / ID: 7yww
TitleMonocot chimeric jacalin JAC1 from Oryza sativa: lectin domain (crystal form 2)
ComponentsDirigent protein
KeywordsPLANT PROTEIN / Monocot chimeric jacalin / Dirigent protein / Lectin / Pathogen resistance
Function / homology
Function and homology information


phenylpropanoid biosynthetic process / apoplast / carbohydrate binding / metal ion binding
Similarity search - Function
Dirigent protein / Dirigent-like protein / Allene oxide cyclase/Dirigent protein / Jacalin-like lectin domain, plant / Jacalin-like lectin domain / Jacalin-type lectin domain profile. / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-like lectin domain superfamily
Similarity search - Domain/homology
IODIDE ION / Dirigent protein
Similarity search - Component
Biological speciesOryza sativa (Asian cultivated rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsHuwa, N. / Classen, T. / Weiergraeber, O.H.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)369034981 Germany
German Research Foundation (DFG)SCHA 631/10-1 Germany
CitationJournal: Biomolecules / Year: 2022
Title: The Crystal Structure of the Defense Conferring Rice Protein Os JAC1 Reveals a Carbohydrate Binding Site on the Dirigent-like Domain.
Authors: Huwa, N. / Weiergraber, O.H. / Fejzagic, A.V. / Kirsch, C. / Schaffrath, U. / Classen, T.
History
DepositionFeb 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dirigent protein
B: Dirigent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,98323
Polymers37,2412
Non-polymers2,74221
Water5,332296
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-19 kcal/mol
Surface area12310 Å2
Unit cell
Length a, b, c (Å)80.320, 99.630, 93.740
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-596-

HOH

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Components

#1: Protein Dirigent protein


Mass: 18620.670 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / Gene: JAC1, LOC_Os12g14440, Os12g0247700, OSNPB_120247700 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q306J3
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.52 Å3/Da / Density % sol: 51.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: PEG 3350, ammonium iodide, potassium phosphate, N-acetylgalactosamine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.919 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919 Å / Relative weight: 1
ReflectionResolution: 1.4→52.02 Å / Num. obs: 71961 / % possible obs: 97.2 % / Redundancy: 3.74 % / Biso Wilson estimate: 22.35 Å2 / CC1/2: 0.999 / Net I/σ(I): 9.65
Reflection shellResolution: 1.4→1.44 Å / Redundancy: 3.74 % / Mean I/σ(I) obs: 0.85 / Num. unique obs: 5441 / CC1/2: 0.501 / % possible all: 99.5

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Processing

Software
NameVersionClassification
XDSdata reduction
MOLREPphasing
PHENIX1.19.2_4158refinement
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PIF

4pif


Resolution: 1.4→46.87 Å / SU ML: 0.2402 / Cross valid method: FREE R-VALUE / Phase error: 24.4977
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1946 3597 5 %
Rwork0.1687 68358 -
obs0.17 71955 97.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.7 Å2
Refinement stepCycle: LAST / Resolution: 1.4→46.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2229 0 38 296 2563
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01312469
X-RAY DIFFRACTIONf_angle_d1.19023374
X-RAY DIFFRACTIONf_chiral_restr0.1071346
X-RAY DIFFRACTIONf_plane_restr0.0107452
X-RAY DIFFRACTIONf_dihedral_angle_d12.2295881
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.52551410.50142690X-RAY DIFFRACTION99.61
1.42-1.440.47751400.47922641X-RAY DIFFRACTION99.22
1.44-1.460.441400.42692662X-RAY DIFFRACTION99.19
1.46-1.480.3941370.41562608X-RAY DIFFRACTION98.04
1.48-1.50.31461380.32912636X-RAY DIFFRACTION98.44
1.5-1.530.36711370.33092595X-RAY DIFFRACTION96.43
1.53-1.550.30881380.28262622X-RAY DIFFRACTION97.63
1.55-1.580.30021390.26622643X-RAY DIFFRACTION99.18
1.58-1.610.28241410.26952670X-RAY DIFFRACTION99.19
1.61-1.650.2661400.25452694X-RAY DIFFRACTION98.92
1.65-1.680.2441380.20942629X-RAY DIFFRACTION98.47
1.68-1.720.23111380.19672620X-RAY DIFFRACTION97.52
1.72-1.760.18411380.17422619X-RAY DIFFRACTION97.77
1.76-1.810.17951370.15892590X-RAY DIFFRACTION96.63
1.81-1.860.17151390.15132638X-RAY DIFFRACTION97
1.86-1.930.19421390.16452642X-RAY DIFFRACTION97.82
1.93-1.990.19611390.14952639X-RAY DIFFRACTION97.99
1.99-2.070.15721380.15062627X-RAY DIFFRACTION97.46
2.07-2.170.16531390.13522623X-RAY DIFFRACTION96.67
2.17-2.280.19721360.13642591X-RAY DIFFRACTION95.32
2.28-2.430.20181360.1472583X-RAY DIFFRACTION95.5
2.43-2.610.16451390.14642636X-RAY DIFFRACTION96.93
2.61-2.880.14791380.1542627X-RAY DIFFRACTION96.01
2.88-3.290.19691350.14652572X-RAY DIFFRACTION93.67
3.29-4.150.19121360.14482598X-RAY DIFFRACTION93.86
4.15-46.870.16111410.16122663X-RAY DIFFRACTION92.09

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