[English] 日本語
Yorodumi
- PDB-6mqu: PL5, synthetic transmembrane domain variant of human phospholamban -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6mqu
TitlePL5, synthetic transmembrane domain variant of human phospholamban
ComponentsPL5, designed TM pentamer
KeywordsDE NOVO PROTEIN / designed / engineered / transmembrane / pentamer / phospholamban
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.17 Å
AuthorsMravic, M. / Thomaston, J.L. / DeGrado, W.F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM054616 United States
CitationJournal: Science / Year: 2019
Title: Packing of apolar side chains enables accurate design of highly stable membrane proteins.
Authors: Mravic, M. / Thomaston, J.L. / Tucker, M. / Solomon, P.E. / Liu, L. / DeGrado, W.F.
History
DepositionOct 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Apr 17, 2019Group: Data collection / Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PL5, designed TM pentamer
B: PL5, designed TM pentamer
C: PL5, designed TM pentamer
D: PL5, designed TM pentamer
E: PL5, designed TM pentamer
F: PL5, designed TM pentamer
G: PL5, designed TM pentamer
H: PL5, designed TM pentamer
I: PL5, designed TM pentamer
J: PL5, designed TM pentamer


Theoretical massNumber of molelcules
Total (without water)38,06710
Polymers38,06710
Non-polymers00
Water1086
1
A: PL5, designed TM pentamer
B: PL5, designed TM pentamer
C: PL5, designed TM pentamer
D: PL5, designed TM pentamer
E: PL5, designed TM pentamer


Theoretical massNumber of molelcules
Total (without water)19,0345
Polymers19,0345
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6070 Å2
ΔGint-94 kcal/mol
Surface area8720 Å2
MethodPISA
2
F: PL5, designed TM pentamer
G: PL5, designed TM pentamer
H: PL5, designed TM pentamer
I: PL5, designed TM pentamer
J: PL5, designed TM pentamer


Theoretical massNumber of molelcules
Total (without water)19,0345
Polymers19,0345
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6080 Å2
ΔGint-94 kcal/mol
Surface area8720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.230, 124.230, 51.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

-
Components

#1: Protein/peptide
PL5, designed TM pentamer


Mass: 3806.718 Da / Num. of mol.: 10 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.63 Å3/Da / Density % sol: 53.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 12 MM C8E4, 20MM MGCL HEXAHYDRATE, 25MM NACL, 50 MM HEPES, 16% PEG400, VAPOR DIFFUSION, TEMPERATURE 298K

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 3.17→87.84 Å / Num. obs: 6819 / % possible obs: 99 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.171 / Net I/σ(I): 6.2
Reflection shellResolution: 3.17→3.39 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1212 / CC1/2: 0.802 / Rpim(I) all: 0.314 / % possible all: 98.2

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
PHENIX(1.11.1_2575: ???)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.17→87.84 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.52
RfactorNum. reflection% reflection
Rfree0.242 675 9.94 %
Rwork0.228 --
obs0.229 6784 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 46.4 Å2
Refinement stepCycle: LAST / Resolution: 3.17→87.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2271 0 0 6 2277
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092322
X-RAY DIFFRACTIONf_angle_d1.1223117
X-RAY DIFFRACTIONf_dihedral_angle_d20.191820
X-RAY DIFFRACTIONf_chiral_restr0.051379
X-RAY DIFFRACTIONf_plane_restr0.004335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.17-3.41480.26551280.23851198X-RAY DIFFRACTION98
3.4148-3.75840.25211370.25721207X-RAY DIFFRACTION99
3.7584-4.30230.24291340.22431226X-RAY DIFFRACTION99
4.3023-5.42030.21871330.20671233X-RAY DIFFRACTION98
5.4203-87.87760.24621420.23051246X-RAY DIFFRACTION98

+
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