[English] 日本語
Yorodumi
- PDB-2qim: Crystal Structure of Pathogenesis-related Protein LlPR-10.2B from... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2qim
TitleCrystal Structure of Pathogenesis-related Protein LlPR-10.2B from yellow lupine in complex with Cytokinin
ComponentsPR10.2B
KeywordsALLERGEN / trans-zeatin / cytokinin / plant hormones / plant protein / PR-10 protein / pathogenesis-related protein
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
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
(2E)-2-methyl-4-(9H-purin-6-ylamino)but-2-en-1-ol / Class 10 plant pathogenesis-related protein 2B
Similarity search - Component
Biological speciesLupinus luteus (yellow lupine)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsFernandes, H.C. / Pasternak, O. / Bujacz, G. / Bujacz, A. / Sikorski, M.M. / Jaskolski, M.
Citation
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.
#1: Journal: Acta Crystallogr.,Sect.D / 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.
#2: 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.
#3: 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.
#4: Journal: Nat.Struct.Biol. / Year: 1996
Title: X-ray and NMR structure of Bet v 1, the origin of birch pollen allergy
Authors: Gajhede, M. / Osmark, P. / Poulsen, F.M. / Ipsen, H. / Larsen, J.N. / Joost van Neerven, R.J. / Schou, C. / Lowenstein, H. / Spangfort, M.D.
#5: Journal: J.Mol.Biol. / Year: 2003
Title: Crystal structure of a hypoallergenic isoform of the major birch pollen allergen Bet v 1 and its likely biological function as a plant steroid carrier.
Authors: Markovic-Housley, Z. / Degano, M. / Lamba, D. / von Roepenack-Lahaye, E. / Clemens, S. / Susani, M. / Ferreira, F. / Scheiner, O. / Breiteneder, H.
History
DepositionJul 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PR10.2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9157
Polymers16,9061
Non-polymers1,0096
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.822, 73.822, 67.212
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

-
Components

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


Mass: 16906.000 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 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS / References: UniProt: Q9LLQ2
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-ZEA / (2E)-2-methyl-4-(9H-purin-6-ylamino)but-2-en-1-ol / TRANS-ZEATIN


Mass: 219.243 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N5O
#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.: 233 / 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: 3.13 Å3/Da / Density % sol: 60.65 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.2 M sodium citrate, 0.1 M MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.803 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 23, 2005 / Details: mirrors
RadiationMonochromator: Si[111], horizontally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.803 Å / Relative weight: 1
ReflectionResolution: 1.35→15 Å / Num. all: 45685 / Num. obs: 45644 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -1 / Redundancy: 9.7 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 56.7
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.5 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: LlPR-10.2F

Resolution: 1.35→15 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.642 / SU ML: 0.03
Isotropic thermal model: Anisotropic displacement parameters for non-H atoms
Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19438 1163 2.5 %RANDOM
Rwork0.14725 ---
obs0.14843 44481 99.99 %-
all-45685 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.218 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å2-0.18 Å20 Å2
2---0.37 Å20 Å2
3---0.55 Å2
Refinement stepCycle: LAST / Resolution: 1.35→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1184 0 71 233 1488
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0241304
X-RAY DIFFRACTIONr_bond_other_d0.0010.02825
X-RAY DIFFRACTIONr_angle_refined_deg2.0432.3321761
X-RAY DIFFRACTIONr_angle_other_deg0.9632052
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8445156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.15526.73152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.49815220
X-RAY DIFFRACTIONr_dihedral_angle_4_deg0.408151
X-RAY DIFFRACTIONr_chiral_restr0.1120.2195
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021425
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02216
X-RAY DIFFRACTIONr_nbd_refined0.2150.2257
X-RAY DIFFRACTIONr_nbd_other0.190.2783
X-RAY DIFFRACTIONr_nbtor_refined0.1940.2643
X-RAY DIFFRACTIONr_nbtor_other0.0890.2696
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.2162
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1520.24
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1020.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1510.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.0531.5801
X-RAY DIFFRACTIONr_mcbond_other3.8931.5325
X-RAY DIFFRACTIONr_mcangle_it6.03121264
X-RAY DIFFRACTIONr_scbond_it9.1673588
X-RAY DIFFRACTIONr_scangle_it11.7024.5497
X-RAY DIFFRACTIONr_rigid_bond_restr4.47732328
X-RAY DIFFRACTIONr_sphericity_free24.1693234
X-RAY DIFFRACTIONr_sphericity_bonded11.3932106
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 84 -
Rwork0.216 3271 -
obs--99.97 %
Refinement TLS params.Method: refined / Origin x: 63.4287 Å / Origin y: 48.9393 Å / Origin z: 0.2718 Å
111213212223313233
T0.0262 Å2-0.0005 Å2-0.0049 Å2-0.0238 Å20.0031 Å2--0.0191 Å2
L0.0783 °20.0484 °20.0043 °2-0.132 °2-0.0309 °2--0.0949 °2
S0.0026 Å °-0.0006 Å °0.0112 Å °-0.0133 Å °0.0074 Å °0.025 Å °0.0054 Å °0.0069 Å °-0.01 Å °

+
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://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