[English] 日本語
Yorodumi
- PDB-1be2: LIPID TRANSFER PROTEIN COMPLEXED WITH PALMITATE, NMR, 10 STRUCTURES -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1be2
TitleLIPID TRANSFER PROTEIN COMPLEXED WITH PALMITATE, NMR, 10 STRUCTURES
ComponentsLIPID TRANSFER PROTEIN
KeywordsLIPID TRANSPORT / LIPID TRANSFER PROTEIN / PALMITATE
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
PALMITIC ACID / Non-specific lipid-transfer protein 1
Similarity search - Component
Biological speciesHordeum vulgare (barley)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsLerche, M.H. / Poulsen, F.M.
Citation
Journal: Protein Sci. / Year: 1998
Title: Solution structure of barley lipid transfer protein complexed with palmitate. Two different binding modes of palmitate in the homologous maize and barley nonspecific lipid transfer proteins.
Authors: Lerche, M.H. / Poulsen, F.M.
#1: Journal: Structure / Year: 1997
Title: Barley Lipid-Transfer Protein Complexed with Palmitoyl Coa: The Structure Reveals a Hydrophobic Binding Site that Can Expand to Fit Both Large and Small Lipid-Like Ligands
Authors: Lerche, M.H. / Kragelund, B.B. / Bech, L.M. / Poulsen, F.M.
#2: Journal: Protein Sci. / Year: 1996
Title: Structure in Solution of a Four-Helix Lipid Binding Protein
Authors: Heinemann, B. / Andersen, K.V. / Nielsen, P.R. / Bech, L.M. / Poulsen, F.M.
#3: Journal: Structure / Year: 1995
Title: High-Resolution Crystal Structure of the Non-Specific Lipid-Transfer Protein from Maize Seedlings
Authors: Shin, D.H. / Lee, J.Y. / Hwang, K.Y. / Kim, K.K. / Suh, S.W.
History
DepositionMay 19, 1998Processing site: BNL
Revision 1.0Dec 2, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_nmr_software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LIPID TRANSFER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9612
Polymers9,7051
Non-polymers2561
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 40LOWEST TOTAL ENERGY
Representative

-
Components

#1: Protein LIPID TRANSFER PROTEIN / LTP


Mass: 9704.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Hordeum vulgare (barley) / Organ: SEEDS / References: UniProt: P07597
#2: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
121TOCSY
131NOESY
141HSQC
151HSQC-NOE

-
Sample preparation

Sample conditionspH: 7.2 / Temperature: 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometerType: Bruker AMX600 / Manufacturer: Bruker / Model: AMX600 / Field strength: 600 MHz

-
Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
X-PLOR3.8phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.8BRUNGERrefinement
Prontostructure solution
X-PLOR3.8structure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
NMR ensembleConformer selection criteria: LOWEST TOTAL ENERGY / Conformers calculated total number: 40 / Conformers submitted total number: 10

+
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