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- PDB-5c9y: Crystal structure of yellow lupine LlPR-10.1A protein partially s... -

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Basic information

Entry
Database: PDB / ID: 5c9y
TitleCrystal structure of yellow lupine LlPR-10.1A protein partially saturated with trans-zeatin
ComponentsProtein LlR18A
KeywordsPLANT PROTEIN / PR-10 FOLD / LIGAND BINDING / PHYTOHORMONE BINDING PROTEIN / TRANS-ZEATIN / CYTOKININ
Function / homology
Function and homology information


cytokinin binding / melatonin binding / abscisic acid binding / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / RNA nuclease activity / defense response / signaling receptor activity / calcium ion binding ...cytokinin binding / melatonin binding / abscisic acid binding / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / RNA nuclease activity / defense response / signaling receptor activity / calcium ion binding / nucleus / cytosol
Similarity search - Function
Pathogenesis-related proteins Bet v I family signature. / Bet v I type allergen / Bet v I/Major latex protein / Pathogenesis-related protein Bet v 1 family / : / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesLupinus luteus (yellow lupine)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSliwiak, J. / Sikorski, M.M. / Jaskolski, M.
CitationJournal: J.Struct.Biol. / Year: 2016
Title: Crystallographic and CD probing of ligand-induced conformational changes in a plant PR-10 protein.
Authors: Sliwiak, J. / Dolot, R. / Michalska, K. / Szpotkowski, K. / Bujacz, G. / Sikorski, M. / Jaskolski, M.
History
DepositionJun 29, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2015Group: Database references
Revision 1.2Jan 13, 2016Group: Database references
Revision 1.3Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Protein LlR18A


Theoretical massNumber of molelcules
Total (without water)16,7491
Polymers16,7491
Non-polymers00
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.506, 57.918, 62.476
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein LlR18A / LlPR10.1A


Mass: 16748.924 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lupinus luteus (yellow lupine) / Gene: LLR18A / Plasmid: PET-3a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P52778
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.92 Å3/Da / Density % sol: 35.86 % / Description: plate
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.8 M (NH4)2SO4, 0.1 M MES, PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.81738 Å
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Jul 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81738 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 21584 / % possible obs: 99.5 % / Redundancy: 7.16 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 21.96
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 7.16 % / Rmerge(I) obs: 0.829 / Mean I/σ(I) obs: 2.45 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX1.7.1-743refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ICX

1icx


Resolution: 1.5→42.48 Å / Cross valid method: FREE R-VALUE
Details: Flat postive electron densities could be observed in the structure indicating the presence of puring rings and tails of three trans-zeatin molecules: two inside protein cavity (one ...Details: Flat postive electron densities could be observed in the structure indicating the presence of puring rings and tails of three trans-zeatin molecules: two inside protein cavity (one interacting with Tyr82 and other with Ser101) and one on the surface of protein (staying in contact with Glu35). However they possess discontinuities and are insufficient for proper ligand modeling thus the structure is deposited without ligand molecules in its coordinates although trans-zeatin was present in crystallization condintions.
RfactorNum. reflection% reflection
Rfree0.2427 --
Rwork0.1814 --
obs-21204 99.6 %
Refinement stepCycle: LAST / Resolution: 1.5→42.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1167 0 0 144 1311
LS refinement shellHighest resolution: 1.5 Å

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