[English] 日本語
Yorodumi
- PDB-6ew5: Human myelin protein P2 F57A mutant, monoclinic crystal form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ew5
TitleHuman myelin protein P2 F57A mutant, monoclinic crystal form
ComponentsMyelin P2 protein
KeywordsLIPID TRANSPORT / fatty acid binding protein / beta barrel / portal region
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 beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PALMITIC ACID / Myelin P2 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLaulumaa, S. / Lehtimaki, M. / Kursula, P.
CitationJournal: BMC Struct. Biol. / Year: 2018
Title: Structure and dynamics of a human myelin protein P2 portal region mutant indicate opening of the beta barrel in fatty acid binding proteins.
Authors: Laulumaa, S. / Nieminen, T. / Raasakka, A. / Krokengen, O.C. / Safaryan, A. / Hallin, E.I. / Brysbaert, G. / Lensink, M.F. / Ruskamo, S. / Vattulainen, I. / Kursula, P.
History
DepositionNov 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Myelin P2 protein
B: Myelin P2 protein
C: Myelin P2 protein
D: Myelin P2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6878
Polymers59,6614
Non-polymers1,0264
Water14,520806
1
A: Myelin P2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1722
Polymers14,9151
Non-polymers2561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Myelin P2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1722
Polymers14,9151
Non-polymers2561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Myelin P2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1722
Polymers14,9151
Non-polymers2561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Myelin P2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1722
Polymers14,9151
Non-polymers2561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.125, 76.105, 138.425
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 14915.374 Da / Num. of mol.: 4 / Mutation: F57A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PMP2 / Production host: Escherichia coli (E. coli) / References: UniProt: P02689
#2: Chemical
ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H32O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 806 / 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: 2.3 Å3/Da / Density % sol: 46.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 40-42% PEG 6000 / PH range: 6-7

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1.1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. obs: 40671 / % possible obs: 99.1 % / Redundancy: 6 % / CC1/2: 0.994 / Rrim(I) all: 0.173 / Rsym value: 0.158 / Net I/σ(I): 11.6
Reflection shellResolution: 1.95→2 Å / Redundancy: 6 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2958 / CC1/2: 0.754 / Rrim(I) all: 0.821 / Rsym value: 0.75 / % possible all: 98.7

-
Processing

Software
NameVersionClassification
PHENIX(dev_2006: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2wut

2wut


Resolution: 1.95→19.49 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.77
RfactorNum. reflection% reflection
Rfree0.2355 2034 5.01 %
Rwork0.1882 --
obs0.1906 40632 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.95→19.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4168 0 72 806 5046
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054357
X-RAY DIFFRACTIONf_angle_d0.9325823
X-RAY DIFFRACTIONf_dihedral_angle_d14.4931730
X-RAY DIFFRACTIONf_chiral_restr0.043674
X-RAY DIFFRACTIONf_plane_restr0.003720
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9496-1.99490.28061320.22972494X-RAY DIFFRACTION98
1.9949-2.04470.26271330.20292523X-RAY DIFFRACTION99
2.0447-2.10.23941340.20062555X-RAY DIFFRACTION99
2.1-2.16170.26941340.20212537X-RAY DIFFRACTION99
2.1617-2.23140.25211300.26292465X-RAY DIFFRACTION97
2.2314-2.3110.3621330.32232527X-RAY DIFFRACTION98
2.311-2.40340.27291330.20132537X-RAY DIFFRACTION100
2.4034-2.51250.24621360.19292580X-RAY DIFFRACTION100
2.5125-2.64470.25611350.19622564X-RAY DIFFRACTION100
2.6447-2.80990.22261360.18662588X-RAY DIFFRACTION100
2.8099-3.02620.25191370.19012582X-RAY DIFFRACTION100
3.0262-3.32930.22631370.16742600X-RAY DIFFRACTION100
3.3293-3.8080.20391380.16092627X-RAY DIFFRACTION100
3.808-4.78590.17341400.13172657X-RAY DIFFRACTION100
4.7859-19.49110.1991460.16772762X-RAY DIFFRACTION100

+
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