[English] 日本語
Yorodumi
- PDB-7nsr: Myelin protein P2 I50del -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7nsr
TitleMyelin protein P2 I50del
ComponentsMyelin P2 protein
KeywordsLIPID BINDING PROTEIN / Membrane binding protein
Function / homology
Function and homology information


membrane organization / cholesterol binding / fatty acid transport / fatty acid binding / myelin sheath / extracellular exosome / nucleus / cytosol
Similarity search - Function
Myelin P2 protein / Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin
Similarity search - Domain/homology
PALMITIC ACID / Myelin P2 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsUusitalo, M. / Ruskamo, S. / Kursula, P.
CitationJournal: Febs J. / Year: 2021
Title: Human myelin protein P2: from crystallography to time-lapse membrane imaging and neuropathy-associated variants.
Authors: Uusitalo, M. / Klenow, M.B. / Laulumaa, S. / Blakeley, M.P. / Simonsen, A.C. / Ruskamo, S. / Kursula, P.
History
DepositionMar 8, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 15, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Myelin P2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2195
Polymers14,8781
Non-polymers3404
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-17 kcal/mol
Surface area7200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.140, 66.140, 101.190
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

-
Components

#1: Protein Myelin P2 protein / Peripheral myelin protein 2


Mass: 14878.313 Da / Num. of mol.: 1 / Mutation: I50del
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PMP2 / Plasmid: pTH27 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P02689
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.49 Å3/Da
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4 / Details: 1.9 M Sodium malonate dibasic monohydrate pH 6.4

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.5→46.77 Å / Num. obs: 36689 / % possible obs: 99.9 % / Redundancy: 13.9 % / Biso Wilson estimate: 26.16 Å2 / CC1/2: 0.999 / Net I/σ(I): 17.64
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 13.69 % / Mean I/σ(I) obs: 1.08 / Num. unique obs: 2657 / CC1/2: 0.743 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NR3

3nr3


Resolution: 1.5→46.77 Å / SU ML: 0.1885 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.9938
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1986 1829 5 %
Rwork0.1818 34756 -
obs0.1827 36585 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.92 Å2
Refinement stepCycle: LAST / Resolution: 1.5→46.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1040 0 21 137 1198
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02151215
X-RAY DIFFRACTIONf_angle_d1.88041634
X-RAY DIFFRACTIONf_chiral_restr0.1297180
X-RAY DIFFRACTIONf_plane_restr0.0117209
X-RAY DIFFRACTIONf_dihedral_angle_d11.0557201
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.43071380.37052606X-RAY DIFFRACTION99.17
1.54-1.590.33251380.31522614X-RAY DIFFRACTION99.28
1.59-1.640.30651370.27632621X-RAY DIFFRACTION99.67
1.64-1.70.23451380.23872630X-RAY DIFFRACTION99.53
1.7-1.760.22641370.21432614X-RAY DIFFRACTION99.49
1.76-1.840.25711390.20312645X-RAY DIFFRACTION99.78
1.84-1.940.21861410.18842661X-RAY DIFFRACTION99.82
1.94-2.060.21611400.1772651X-RAY DIFFRACTION99.79
2.06-2.220.17321390.16852669X-RAY DIFFRACTION99.86
2.22-2.450.20381420.16832695X-RAY DIFFRACTION100
2.45-2.80.18771420.1912702X-RAY DIFFRACTION99.96
2.8-3.530.21681450.19072744X-RAY DIFFRACTION100
3.53-46.770.1661530.1572904X-RAY DIFFRACTION99.97

+
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://pdbjlvh1.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