[English] 日本語
Yorodumi
- PDB-2b5s: Crystal structure of peach Pru p3, the prototypic member of the f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2b5s
TitleCrystal structure of peach Pru p3, the prototypic member of the family of plant non-specific lipid transfer protein pan-allergens
ComponentsNon-specific lipid transfer protein
KeywordsLIPID TRANSPORT / non-specific lipid transfer protein / ns-ltp / food allergen
Function / homology
Function and homology information


lipid transport / lipid binding
Similarity search - Function
Plant lipid transfer proteins signature. / Plant non-specific lipid-transfer protein/Par allergen / Plant lipid-transfer and hydrophobic proteins / Hydrophobic Seed Protein / Protease inhibitor/seed storage/LTP family / Plant lipid transfer protein / seed storage protein / trypsin-alpha amylase inhibitor domain family / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
LAURIC ACID / HEPTANE / Non-specific lipid-transfer protein 1
Similarity search - Component
Biological speciesPrunus persica (peach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsPasquato, N. / Berni, R. / Folli, C. / Folloni, S. / Cianci, M. / Pantano, S. / Helliwell, R.J. / Zanotti, G.
Citation
Journal: J.Mol.Biol. / Year: 2006
Title: Crystal Structure of Peach Pru p 3, the Prototypic Member of the Family of Plant Non-specific Lipid Transfer Protein Pan-allergens
Authors: Pasquato, N. / Berni, R. / Folli, C. / Folloni, S. / Cianci, M. / Pantano, S. / Helliwell, J.R. / Zanotti, G.
#1: Journal: Structure / Year: 1995
Title: High-resolution crystal structure of the non-specific lipid-transfer protein from maize seedling
Authors: Shin, D.H. / Lee, J.Y. / Hwang, K.Y. / Kim, K.K. / Suk, S.W.
#2: Journal: J.Allergy Clin.Immunol. / Year: 2003
Title: Identification of IgE-binding epitopes of the major peach allergen Pru p 3
Authors: Garcia-Casado, G. / Pacios, F.L. / Diaz-Perales, A. / Sanchez-Monge, R. / Lombardero, M. / Garcia-Selles, J.F. / Polo, F. / Barber, D. / Salcedo, G.
History
DepositionSep 29, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Non-specific lipid transfer protein
B: Non-specific lipid transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1626
Polymers18,5652
Non-polymers5974
Water2,666148
1
A: Non-specific lipid transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5833
Polymers9,2831
Non-polymers3012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Non-specific lipid transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5793
Polymers9,2831
Non-polymers2962
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Non-specific lipid transfer protein
hetero molecules

A: Non-specific lipid transfer protein
hetero molecules

B: Non-specific lipid transfer protein
hetero molecules

B: Non-specific lipid transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,32512
Polymers37,1314
Non-polymers1,1948
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_554-x+y,y,-z-1/21
crystal symmetry operation5_555y,-x+y,z+1/61
crystal symmetry operation9_554-x,-x+y,-z-2/31
Buried area8020 Å2
ΔGint-42 kcal/mol
Surface area15130 Å2
MethodPISA
4
A: Non-specific lipid transfer protein
hetero molecules

B: Non-specific lipid transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1626
Polymers18,5652
Non-polymers5974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_554-x,-x+y,-z-2/31
Buried area2910 Å2
ΔGint-14 kcal/mol
Surface area8660 Å2
MethodPISA
5
B: Non-specific lipid transfer protein
hetero molecules

B: Non-specific lipid transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1586
Polymers18,5652
Non-polymers5934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-5/61
Buried area1040 Å2
ΔGint-28 kcal/mol
Surface area9270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.352, 102.352, 74.236
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11B-249-

HOH

-
Components

#1: Protein Non-specific lipid transfer protein


Mass: 9282.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Prunus persica (peach) / Gene: LTP / Plasmid: pET11b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Origami (DE3) / References: UniProt: P81402
#2: Chemical ChemComp-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H24O2
#3: Chemical ChemComp-HP6 / HEPTANE


Mass: 100.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: ammonium sulphate 2.3 M, Sodium acetate 0.1 M, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.957 Å
DetectorType: SBC-2 / Detector: CCD / Date: Oct 22, 2004
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.957 Å / Relative weight: 1
ReflectionResolution: 2.35→44.32 Å / Num. obs: 10082 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.8 % / Biso Wilson estimate: 38.1 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 37.8
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 11 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 4.1 / Num. unique all: 976 / Rsym value: 0.66 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2ALG

2alg


Resolution: 2.35→44.32 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1741035.68 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.263 728 7.3 %RANDOM
Rwork0.216 ---
obs0.216 10001 99.9 %-
all-10019 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 67.5397 Å2 / ksol: 0.350052 e/Å3
Displacement parametersBiso mean: 49.4 Å2
Baniso -1Baniso -2Baniso -3
1--3.89 Å21.05 Å20 Å2
2---3.89 Å20 Å2
3---7.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.35→44.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1284 0 40 148 1472
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_improper_angle_d0.94
LS refinement shellResolution: 2.35→2.5 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.272 110 6.8 %
Rwork0.229 1509 -
obs--99.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top
X-RAY DIFFRACTION3ligand_tot.paramligand_tot.top

+
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