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- PDB-7ywe: Monocot chimeric jacalin JAC1 from Oryza sativa: dirigent domain ... -

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Basic information

Entry
Database: PDB / ID: 7ywe
TitleMonocot chimeric jacalin JAC1 from Oryza sativa: dirigent 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
PHOSPHATE ION / Dirigent protein
Similarity search - Component
Biological speciesOryza sativa (Asian cultivated rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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 13, 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

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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
C: Dirigent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8548
Polymers52,3563
Non-polymers4985
Water46826
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)158.900, 158.900, 47.850
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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Components

#1: Protein Dirigent protein


Mass: 17452.025 Da / Num. of mol.: 3
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.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.22 Å3/Da / Density % sol: 44.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: ammonium dihydrogen phosphate, Tris-HCl, methylpentanediol, dithiothreitol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.15→45.87 Å / Num. obs: 24426 / % possible obs: 99.7 % / Redundancy: 4.22 % / Biso Wilson estimate: 60.84 Å2 / CC1/2: 0.998 / Net I/σ(I): 7.83
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 4.36 % / Mean I/σ(I) obs: 0.68 / Num. unique obs: 1815 / CC1/2: 0.353 / % possible all: 99.9

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Processing

Software
NameVersionClassification
XDSdata reduction
MoRDaphasing
PHENIX1.19.2_4158refinement
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OOD

6ood


Resolution: 2.15→45.87 Å / SU ML: 0.4596 / Cross valid method: FREE R-VALUE / Phase error: 41.8232
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2544 1219 5.01 %
Rwork0.2178 23128 -
obs0.2196 24347 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 80.34 Å2
Refinement stepCycle: LAST / Resolution: 2.15→45.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3204 0 28 26 3258
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00163297
X-RAY DIFFRACTIONf_angle_d0.45974485
X-RAY DIFFRACTIONf_chiral_restr0.0427506
X-RAY DIFFRACTIONf_plane_restr0.0028572
X-RAY DIFFRACTIONf_dihedral_angle_d11.20921105
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.240.51911350.53972552X-RAY DIFFRACTION99.48
2.24-2.340.52751370.46992569X-RAY DIFFRACTION98.83
2.34-2.460.4921330.4372556X-RAY DIFFRACTION99.26
2.46-2.620.38581360.3412576X-RAY DIFFRACTION99.45
2.62-2.820.37611370.29652613X-RAY DIFFRACTION99.78
2.82-3.10.3321350.24392554X-RAY DIFFRACTION99.81
3.1-3.550.22551340.182554X-RAY DIFFRACTION98.93
3.55-4.470.19011360.1642580X-RAY DIFFRACTION99.05
4.47-45.870.20921360.18322574X-RAY DIFFRACTION99.82
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.55492903311-0.0691423068858-0.8984729921463.89324907950.01039663511330.5726101018860.00647988015637-0.17461053840.2696028122590.131555594797-0.07336070022130.316619449687-0.0752351146544-0.1304895952940.06679203962430.620833735518-0.0443796911895-0.06691587937820.613881171942-0.03450347244490.639753750542.079392367569.806239145223.5099791086
22.011885031120.193059466807-1.379005628689.829557679150.4615038494626.83279638649-0.9984022477221.131527041230.0927795268305-0.824877371187-0.342622301933-0.07122997842410.436313833253-0.2730204527240.8538537555730.805741925711-0.08353507471790.0003497361129120.853097605082-0.007132633310560.8560401775867.108848380477.50172819435.6856955527
31.749369501140.6029079457520.7715384373062.88700137433-0.05076687729231.72105010233-0.07304056189250.441146305709-0.326473434515-0.7251471001120.100144704902-0.1948553095230.03997273576030.0641544428797-0.01186699247380.859453894714-0.04406307922670.04834212769560.699996275977-0.0612476720830.88951764071144.499978189752.84793392757.48485523099
42.684057518040.5761969985230.1424563195123.82153739103-0.9748197260161.90816644662-0.125928044595-0.0887873208032-0.379857492891-0.0915636794361-0.105405533646-0.7731406741980.07718475985290.3684891128920.2603793379880.679354968695-0.0008620424207870.07059316741560.7044754384280.04626872641411.0701571192463.68044193462.43683299417.4349130347
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 19 through 156 )AA19 - 1561 - 138
22chain 'B' and (resid 5 through 14 )BD5 - 141 - 10
33chain 'B' and (resid 15 through 156 )BD15 - 15611 - 152
44chain 'C' and (resid 15 through 156 )CF15 - 1561 - 142

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