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

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Basic information

Entry
Database: PDB / ID: 7ywg
TitleMonocot chimeric jacalin JAC1 from Oryza sativa: lectin domain (crystal form 1)
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
PHOSPHATE ION / Dirigent protein
Similarity search - Component
Biological speciesOryza sativa (Asian cultivated rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 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 20, 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)36,9103
Polymers36,8152
Non-polymers951
Water7,782432
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-22 kcal/mol
Surface area12730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.930, 63.510, 105.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Dirigent protein


Mass: 18407.408 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 432 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: PEG 3350, MES, potassium phosphate, sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97879 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97879 Å / Relative weight: 1
ReflectionResolution: 1.1→54.46 Å / Num. obs: 87556 / % possible obs: 90.9 % / Redundancy: 2.25 % / Biso Wilson estimate: 13.34 Å2 / CC1/2: 0.988 / Net I/σ(I): 5.45
Reflection shellResolution: 1.1→1.13 Å / Redundancy: 1.35 % / Mean I/σ(I) obs: 0.85 / Num. unique obs: 3988 / CC1/2: 0.612 / % possible all: 56.7

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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: 1.1→54.46 Å / SU ML: 0.1284 / Cross valid method: FREE R-VALUE / Phase error: 20.8595
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.188 4377 5 %
Rwork0.1551 83173 -
obs0.1568 87550 90.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.56 Å2
Refinement stepCycle: LAST / Resolution: 1.1→54.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2237 0 5 432 2674
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00752522
X-RAY DIFFRACTIONf_angle_d1.03063466
X-RAY DIFFRACTIONf_chiral_restr0.0929355
X-RAY DIFFRACTIONf_plane_restr0.0071468
X-RAY DIFFRACTIONf_dihedral_angle_d12.4633900
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.110.3784820.34221563X-RAY DIFFRACTION51.73
1.11-1.130.3451970.31741839X-RAY DIFFRACTION60.56
1.13-1.140.33441010.29121928X-RAY DIFFRACTION65.22
1.14-1.150.33231140.27522161X-RAY DIFFRACTION71.21
1.15-1.170.33831250.25992364X-RAY DIFFRACTION79.04
1.17-1.190.30571350.24892582X-RAY DIFFRACTION85.85
1.19-1.20.27921490.23172826X-RAY DIFFRACTION93.06
1.2-1.220.26791560.20572953X-RAY DIFFRACTION98.7
1.22-1.240.23831570.20522979X-RAY DIFFRACTION98.46
1.24-1.260.25671560.19422968X-RAY DIFFRACTION98.24
1.26-1.280.25381560.1882967X-RAY DIFFRACTION98.58
1.28-1.310.23121550.17382945X-RAY DIFFRACTION97.51
1.31-1.330.21381510.18052895X-RAY DIFFRACTION95.46
1.33-1.360.261570.17072977X-RAY DIFFRACTION98.71
1.36-1.390.19091580.16232998X-RAY DIFFRACTION99.03
1.39-1.420.19691580.15383002X-RAY DIFFRACTION99
1.42-1.450.20161580.1522997X-RAY DIFFRACTION98.19
1.45-1.490.21281550.14582945X-RAY DIFFRACTION97.64
1.49-1.540.1981510.14252887X-RAY DIFFRACTION95.12
1.54-1.590.19251570.13672968X-RAY DIFFRACTION96.48
1.59-1.640.18641560.13142975X-RAY DIFFRACTION98.46
1.64-1.710.18691570.14032974X-RAY DIFFRACTION97.66
1.71-1.790.18191570.14662986X-RAY DIFFRACTION97.88
1.79-1.880.20611550.15152950X-RAY DIFFRACTION96.46
1.88-20.16181520.1332888X-RAY DIFFRACTION93.71
2-2.150.17661560.13162954X-RAY DIFFRACTION96.02
2.15-2.370.17251560.14632965X-RAY DIFFRACTION95.33
2.37-2.710.17851520.15682900X-RAY DIFFRACTION93.19
2.71-3.420.1611530.14392901X-RAY DIFFRACTION92.18
3.42-54.460.15861550.14892936X-RAY DIFFRACTION88.54

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