[English] 日本語
Yorodumi
- PDB-5mxb: Crystal structure of yellow lupin LLPR-10.2B protein in complex w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5mxb
TitleCrystal structure of yellow lupin LLPR-10.2B protein in complex with melatonin
ComponentsClass 10 plant pathogenesis-related protein
KeywordsPLANT PROTEIN / phytohormon binding protein / PR-10 protein / melatonin
Function / homology
Function and homology information


cytokinin binding / response to biotic stimulus / 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 ...cytokinin binding / response to biotic stimulus / 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
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
N-[2-(5-methoxy-1H-indol-3-yl)ethyl]acetamide / Unknown ligand / Class 10 plant pathogenesis-related protein 2B
Similarity search - Component
Biological speciesLupinus luteus (yellow lupine)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsSliwiak, J. / Sikorski, M. / Jaskolski, M.
Funding support2items
OrganizationGrant numberCountry
BioStruct-X283570
European UnionFP7/2007-20013
Citation
Journal: FEBS J. / Year: 2018
Title: PR-10 proteins as potential mediators of melatonin-cytokinin cross-talk in plants: crystallographic studies of LlPR-10.2B isoform from yellow lupine.
Authors: Sliwiak, J. / Sikorski, M. / Jaskolski, M.
#2: Journal: Front Plant Sci / Year: 2016
Title: Crystal Structure of Hyp-1, a Hypericum perforatum PR-10 Protein, in Complex with Melatonin.
Authors: Sliwiak, J. / Dauter, Z. / Jaskolski, M.
#3: Journal: 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.
#4: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2014
Title: Specific binding of gibberellic acid by cytokinin-specific binding proteins: a new aspect of plant hormone-binding proteins with the PR-10 fold.
Authors: Ruszkowski, M. / Sliwiak, J. / Ciesielska, A. / Barciszewski, J. / Sikorski, M. / Jaskolski, M.
#5: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2015
Title: ANS complex of St John's wort PR-10 protein with 28 copies in the asymmetric unit: a fiendish combination of pseudosymmetry with tetartohedral twinning.
Authors: Sliwiak, J. / Dauter, Z. / Kowiel, M. / McCoy, A.J. / Read, R.J. / Jaskolski, M.
#6: Journal: FEBS J. / Year: 2009
Title: Cytokinin-induced structural adaptability of a Lupinus luteus PR-10 protein.
Authors: Fernandes, H. / Bujacz, A. / Bujacz, G. / Jelen, F. / Jasinski, M. / Kachlicki, P. / Otlewski, J. / Sikorski, M.M. / Jaskolski, M.
#7: Journal: J. Mol. Biol. / Year: 2008
Title: Lupinus luteus pathogenesis-related protein as a reservoir for cytokinin.
Authors: Fernandes, H. / Pasternak, O. / Bujacz, G. / Bujacz, A. / Sikorski, M.M. / Jaskolski, M.
#8: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2005
Title: Structure of a yellow lupin pathogenesis-related PR-10 protein belonging to a novel subclass.
Authors: Pasternak, O. / Biesiadka, J. / Dolot, R. / Handschuh, L. / Bujacz, G. / Sikorski, M.M. / Jaskolski, M.
#9: Journal: J. Mol. Biol. / Year: 2002
Title: Crystal structures of two homologous pathogenesis-related proteins from yellow lupine.
Authors: Biesiadka, J. / Bujacz, G. / Sikorski, M.M. / Jaskolski, M.
#10: Journal: Plant Cell / Year: 2006
Title: Crystal structure of Vigna radiata cytokinin-specific binding protein in complex with zeatin.
Authors: Pasternak, O. / Bujacz, G.D. / Fujimoto, Y. / Hashimoto, Y. / Jelen, F. / Otlewski, J. / Sikorski, M.M. / Jaskolski, M.
#11: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2013
Title: The landscape of cytokinin binding by a plant nodulin.
Authors: Ruszkowski, M. / Szpotkowski, K. / Sikorski, M. / Jaskolski, M.
History
DepositionJan 22, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Aug 8, 2018Group: Data collection / Database references / Category: pdbx_related_exp_data_set / Item: _pdbx_related_exp_data_set.data_reference
Revision 1.3Jan 17, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Class 10 plant pathogenesis-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,98523
Polymers16,4981
Non-polymers48822
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-2 kcal/mol
Surface area8330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.469, 74.469, 67.110
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

-
Components

#1: Protein Class 10 plant pathogenesis-related protein / PR10.2B


Mass: 16497.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lupinus luteus (yellow lupine) / Gene: pr10.2b, Ypr10.2b / Production host: Escherichia coli (E. coli) / References: UniProt: Q9LLQ2
#2: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 19 / Source method: obtained synthetically
#3: Chemical ChemComp-ML1 / N-[2-(5-methoxy-1H-indol-3-yl)ethyl]acetamide / Melatonin


Mass: 232.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H16N2O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.26 Å3/Da / Density % sol: 62.22 % / Description: prism
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.3 / Details: 1.4 M sodium citrate pH 6.3

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.51→37.23 Å / Num. obs: 33163 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.069 % / Biso Wilson estimate: 30.38 Å2 / Rmerge(I) obs: 0.04 / Rrim(I) all: 0.047 / Χ2: 0.932 / Net I/σ(I): 18.48
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRrim(I) all% possible all
1.51-1.63.9980.6952.1853440.80399.4
1.6-1.714.0760.3883.9750040.44899.9
1.71-1.854.0980.1957.3346800.22599.9
1.85-2.024.1060.0815.5343160.093100
2.02-2.264.1040.04824.5239310.05599.9
2.26-2.614.1320.03830.6734310.044100
2.61-3.24.0950.03239.1229280.03799.7
3.2-4.514.020.02846.5522580.03299.2
4.51-37.233.8470.03146.3112710.03798.4

-
Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2qim

2qim


Resolution: 1.51→37.23 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.681 / SU ML: 0.048 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.065 / ESU R Free: 0.068
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2107 1095 3.3 %RANDOM
Rwork0.1829 ---
obs0.1838 32068 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 82.07 Å2 / Biso mean: 29.189 Å2 / Biso min: 10.96 Å2
Baniso -1Baniso -2Baniso -3
1--0.81 Å2-0.81 Å20 Å2
2---0.81 Å20 Å2
3---2.63 Å2
Refinement stepCycle: final / Resolution: 1.51→37.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1163 0 54 150 1367
Biso mean--40.9 38.82 -
Num. residues----155
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191294
X-RAY DIFFRACTIONr_bond_other_d0.0010.021236
X-RAY DIFFRACTIONr_angle_refined_deg1.9332.0021760
X-RAY DIFFRACTIONr_angle_other_deg0.79332877
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7935171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.8526.850
X-RAY DIFFRACTIONr_dihedral_angle_3_deg1415222
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.784151
X-RAY DIFFRACTIONr_chiral_restr0.1150.2194
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.021504
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02263
LS refinement shellResolution: 1.51→1.549 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 80 -
Rwork0.267 2345 -
all-2425 -
obs--98.74 %
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)
13.4802-2.87271.12284.5785-1.18451.6880.06110.048-0.2106-0.25270.13250.32630.0781-0.0056-0.19370.11970.0006-0.04610.09190.00690.038927.8271-16.3569-8.26
21.17410.2692-0.21551.0416-0.59921.13090.0531-0.0940.11990.04410.01560.1702-0.103-0.0289-0.06870.0816-0.0091-0.01110.0716-0.00860.045324.753-10.56656.8338
31.55120.07240.22283.2984-3.61185.21720.131-0.1131-0.052-0.1779-0.02590.05680.15130.204-0.10510.1191-0.0122-0.01210.09280.00010.004232.229-14.39134.8002
42.6707-1.50570.63223.2322-1.05991.510.05630.1177-0.1433-0.03180.01380.15040.00290.2724-0.070.160.0233-0.03760.1247-0.02050.018734.0636-19.1385-2.825
54.6366-2.6423-0.62254.04040.35390.81680.01820.21840.1456-0.3884-0.04220.18840.0359-0.04680.0240.0988-0.0086-0.02040.08270.02630.045120.1309-19.5466-2.1799
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 17
2X-RAY DIFFRACTION2A18 - 76
3X-RAY DIFFRACTION3A77 - 90
4X-RAY DIFFRACTION4A91 - 126
5X-RAY DIFFRACTION5A127 - 155

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more