[English] 日本語
Yorodumi
- PDB-6fdb: Positively supercharged variant of the computationally designed c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6fdb
TitlePositively supercharged variant of the computationally designed cage protein O3-33
ComponentsPropanediol utilization protein
KeywordsDE NOVO PROTEIN / computationally designed cage protein / O3-33
Function / homology
Function and homology information


Bacterial microcompartment shell protein PduT / BMC (bacterial microcompartment) domain / BMC domain / Bacterial microcompartment domain / CcmK-like superfamily / BMC / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BMC domain-containing protein
Similarity search - Component
Biological speciesSalmonella choleraesuis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.619 Å
AuthorsEdwardson, T. / Mori, T. / Hilvert, D.
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: Rational Engineering of a Designed Protein Cage for siRNA Delivery.
Authors: Edwardson, T.G.W. / Mori, T. / Hilvert, D.
History
DepositionDec 22, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Propanediol utilization protein
B: Propanediol utilization protein
C: Propanediol utilization protein
D: Propanediol utilization protein
E: Propanediol utilization protein
F: Propanediol utilization protein
G: Propanediol utilization protein
H: Propanediol utilization protein


Theoretical massNumber of molelcules
Total (without water)161,0678
Polymers161,0678
Non-polymers00
Water0
1
A: Propanediol utilization protein
B: Propanediol utilization protein
C: Propanediol utilization protein
D: Propanediol utilization protein
E: Propanediol utilization protein
G: Propanediol utilization protein
H: Propanediol utilization protein

A: Propanediol utilization protein
B: Propanediol utilization protein
C: Propanediol utilization protein
D: Propanediol utilization protein
E: Propanediol utilization protein
G: Propanediol utilization protein
H: Propanediol utilization protein

A: Propanediol utilization protein
B: Propanediol utilization protein
C: Propanediol utilization protein
D: Propanediol utilization protein
E: Propanediol utilization protein
G: Propanediol utilization protein
H: Propanediol utilization protein

F: Propanediol utilization protein

F: Propanediol utilization protein

F: Propanediol utilization protein


Theoretical massNumber of molelcules
Total (without water)483,20124
Polymers483,20124
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_565x-y,-y+1,-z1
crystal symmetry operation6_665-x+1,-x+y+1,-z1
Buried area61310 Å2
ΔGint-304 kcal/mol
Surface area153680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.865, 136.865, 559.097
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

-
Components

#1: Protein
Propanediol utilization protein


Mass: 20133.373 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: Mutation with respect to O3-33: T11R, P39R, E66R, W103R, F130R, L163R
Source: (gene. exp.) Salmonella choleraesuis (bacteria)
Gene: A7S24_10320, A7S72_11360, BUJ19_10850, CBI64_04620, CEP91_14370, IN36_13565, IN77_10790, IN95_23850, NGUA18_00608
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M0QF47

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2 M (NH4)2SO4, 5% 2-propanol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.619→50 Å / Num. obs: 44350 / % possible obs: 99.5 % / Redundancy: 6 % / CC1/2: 0.989 / Rmerge(I) obs: 0.308 / Net I/σ(I): 5.3
Reflection shellResolution: 3.619→3.84 Å / Rmerge(I) obs: 1.892 / Mean I/σ(I) obs: 0.89 / Num. unique obs: 6952 / CC1/2: 0.341 / % possible all: 97.4

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VCD

3vcd


Resolution: 3.619→47.594 Å / SU ML: 0.69 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.89
RfactorNum. reflection% reflection
Rfree0.2877 2225 5.02 %
Rwork0.2254 --
obs0.2285 44319 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.619→47.594 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10624 0 0 0 10624
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310720
X-RAY DIFFRACTIONf_angle_d0.59814496
X-RAY DIFFRACTIONf_dihedral_angle_d16.8453896
X-RAY DIFFRACTIONf_chiral_restr0.0431800
X-RAY DIFFRACTIONf_plane_restr0.0031840
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6192-3.69790.4471340.39712478X-RAY DIFFRACTION93
3.6979-3.78390.4081420.37152613X-RAY DIFFRACTION100
3.7839-3.87840.3611400.34372651X-RAY DIFFRACTION100
3.8784-3.98330.38621380.33172607X-RAY DIFFRACTION100
3.9833-4.10040.37311390.30342618X-RAY DIFFRACTION100
4.1004-4.23270.36061440.29782679X-RAY DIFFRACTION100
4.2327-4.38390.35661390.28482648X-RAY DIFFRACTION100
4.3839-4.55920.35361390.25752650X-RAY DIFFRACTION100
4.5592-4.76660.27651390.23622624X-RAY DIFFRACTION100
4.7666-5.01760.26951410.21932650X-RAY DIFFRACTION100
5.0176-5.33160.33381360.23982637X-RAY DIFFRACTION100
5.3316-5.74260.28961400.24682649X-RAY DIFFRACTION100
5.7426-6.31930.32641370.23522652X-RAY DIFFRACTION100
6.3193-7.2310.2751420.19172663X-RAY DIFFRACTION100
7.231-9.09990.1611390.13482634X-RAY DIFFRACTION100
9.0999-47.59770.25791360.17592641X-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