[English] 日本語
Yorodumi
- PDB-1t27: THE STRUCTURE OF PITP COMPLEXED TO PHOSPHATIDYLCHOLINE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1t27
TitleTHE STRUCTURE OF PITP COMPLEXED TO PHOSPHATIDYLCHOLINE
ComponentsPhosphatidylinositol transfer protein alpha isoform
KeywordsLIPID BINDING PROTEIN
Function / homology
Function and homology information


stearic acid binding / phosphatidylcholine transporter activity / phosphatidylcholine transfer activity / phosphatidylinositol transfer activity / fatty-acyl-CoA binding / phospholipid transport / phosphatidylcholine binding / phosphatidylinositol binding / axonogenesis / phospholipid binding ...stearic acid binding / phosphatidylcholine transporter activity / phosphatidylcholine transfer activity / phosphatidylinositol transfer activity / fatty-acyl-CoA binding / phospholipid transport / phosphatidylcholine binding / phosphatidylinositol binding / axonogenesis / phospholipid binding / lipid binding / nucleus / cytoplasm
Similarity search - Function
: / Phosphatidylinositol transfer protein / Phosphatidylinositol transfer protein / 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
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Phosphatidylinositol transfer protein alpha isoform
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsYoder, M.D. / Thomas, L.M. / Tremblay, J.M. / Oliver, R.L. / Yarbrough, L.R. / Helmkamp Jr., G.M.
Citation
Journal: J.Biol.Chem. / Year: 2001
Title: STRUCTURE OF A MULTIFUNCTIONAL PROTEIN. MAMMALIAN PHOSPHATIDYLINOSITOL TRANSFER PROTEIN COMPLEXED WITH PHOSPHATIDYLCHOLINE
Authors: Yoder, M.D. / Thomas, L.M. / Tremblay, J.M. / Oliver, R.L. / Yarbrough, L.R. / Helmkamp Jr., G.M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: X-RAY ANALYSIS OF CRYSTALS OF RAT PHOSPHATIDYLINOSITOL-TRANSFER PROTEIN WITH BOUND PHOSPHATIDYLCHOLINE
Authors: Oliver, R.L. / Tremblay, J.M. / Helmkamp Jr., G.M. / Yarbrough, L.R. / Breakfield, N.W. / Yoder, M.D.
History
DepositionApr 20, 2004Deposition site: RCSB / Processing site: RCSB
SupersessionMay 11, 2004ID: 1FVZ
Revision 1.0May 11, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphatidylinositol transfer protein alpha isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7432
Polymers31,9551
Non-polymers7871
Water2,594144
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.914, 73.773, 48.185
Angle α, β, γ (deg.)90.00, 114.73, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Phosphatidylinositol transfer protein alpha isoform / PtdIns transfer protein alpha / PtdInsTP / PI-TP-alpha


Mass: 31955.451 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: PITPN, PITPNA / Organ: brain / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P16446
#2: Chemical ChemComp-PCW / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / (Z,Z)-4-HYDROXY-N,N,N-TRIMETHYL-10-OXO-7-[(1-OXO-9-OCTADECENYL)OXY]-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-18-EN-1-AMINIUM-4-OXIDE


Mass: 787.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H85NO8P / Comment: DOPC, phospholipid*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.25 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG 4000, sodium acetate, Tris-HCL, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9791, 0.9794, 0.9500
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Nov 18, 1999
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97941
30.951
ReflectionResolution: 2.2→50 Å / Num. all: 38629 / Num. obs: 38629 / % possible obs: 90.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 7.4 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 20.2
Reflection shellResolution: 2.2→50 Å / Rmerge(I) obs: 0.081 / % possible all: 67.2

-
Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→19.94 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1407892.84 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.25 629 5.2 %RANDOM
Rwork0.205 ---
all0.205 13081 --
obs0.205 12145 85.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.3224 Å2 / ksol: 0.338776 e/Å3
Displacement parametersBiso mean: 21.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.1 Å20 Å20.99 Å2
2---2.08 Å20 Å2
3----0.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2231 0 54 144 2429
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.751.5
X-RAY DIFFRACTIONc_mcangle_it2.82
X-RAY DIFFRACTIONc_scbond_it2.482
X-RAY DIFFRACTIONc_scangle_it3.862.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.288 67 4.6 %
Rwork0.202 1396 -
obs--62.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PCO.PARPCO.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.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