[English] 日本語
Yorodumi
- PDB-1tuk: Crystal structure of liganded type 2 non specific lipid transfer ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1tuk
TitleCrystal structure of liganded type 2 non specific lipid transfer protein from wheat
ComponentsNonspecific lipid-transfer protein 2G
KeywordsLIPID TRANSPORT / ns-LTP2 / lipid transfer protein
Function / homology
Function and homology information


lipid transport / cell wall organization / lipid binding / extracellular region
Similarity search - Function
Non-specific lipid-transfer protein type 2 / Plant lipid-transfer and hydrophobic proteins / Hydrophobic Seed Protein / Protease inhibitor/seed storage/LTP 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
IODIDE ION / Chem-PGM / Non-specific lipid-transfer protein 2G
Similarity search - Component
Biological speciesTriticum aestivum (bread wheat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.12 Å
AuthorsHoh, F. / Pons, J.L. / Gautier, M.F. / De Lamotte, F. / Dumas, C.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Structure of a liganded type 2 non-specific lipid-transfer protein from wheat and the molecular basis of lipid binding.
Authors: Hoh, F. / Pons, J.L. / Gautier, M.F. / de Lamotte, F. / Dumas, C.
#1: Journal: J.BIOL.CHEM. / Year: 2003
Title: Refined solution structure of a liganded type 2 wheat nonspecific lipid transfer protein
Authors: Pons, J.L. / de Lamotte, F. / Gautier, M.F. / Delsuc, M.A.
History
DepositionJun 25, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 28, 2016Group: Structure summary
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nonspecific lipid-transfer protein 2G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2075
Polymers6,9861
Non-polymers1,2214
Water1,35175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.465, 29.320, 41.550
Angle α, β, γ (deg.)90.00, 127.65, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Nonspecific lipid-transfer protein 2G / ns-LTP2 / LTP2G / Lipid transfer protein 2 isoform 1 / LTP2-1 / 7 kDa lipid transfer protein 1


Mass: 6985.943 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: P82900
#2: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-PGM / 1-MYRISTOYL-2-HYDROXY-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)] / LYSOPHOSPHATIDYLGLYCEROL


Mass: 483.553 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H44O9P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 1.91 Å3/Da / Density % sol: 35.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.8 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 16, 2002
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.12→32.97 Å / Num. all: 22535 / Num. obs: 22535 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.123→1.153 Å / % possible all: 79.71

-
Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SnBphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.12→32.9 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.855 / SU ML: 0.018 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.032 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.162 1097 5.1 %RANDOM
Rwork0.137 ---
all0.138 21350 --
obs0.138 22496 94.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20.37 Å2
2---0.58 Å20 Å2
3---0.8 Å2
Refinement stepCycle: LAST / Resolution: 1.12→32.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms483 0 44 75 602
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.021551
X-RAY DIFFRACTIONr_bond_other_d0.0030.02500
X-RAY DIFFRACTIONr_angle_refined_deg1.9372.017738
X-RAY DIFFRACTIONr_angle_other_deg3.49331181
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.336566
X-RAY DIFFRACTIONr_dihedral_angle_2_deg46.85523.63622
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.831580
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.839154
X-RAY DIFFRACTIONr_chiral_restr0.1280.275
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02590
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02100
X-RAY DIFFRACTIONr_nbd_refined0.3030.2144
X-RAY DIFFRACTIONr_nbd_other0.2470.2491
X-RAY DIFFRACTIONr_nbtor_refined0.1870.2262
X-RAY DIFFRACTIONr_nbtor_other0.0930.2303
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.4010.277
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.660.228
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3880.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4560.229
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3131.5339
X-RAY DIFFRACTIONr_mcbond_other1.3251.5138
X-RAY DIFFRACTIONr_mcangle_it3.192533
X-RAY DIFFRACTIONr_scbond_it4.4423225
X-RAY DIFFRACTIONr_scangle_it6.1244.5205
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.123→1.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 55 -
Rwork0.253 1269 -
obs--79.71 %

+
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