[English] 日本語
Yorodumi
- PDB-7sj5: Bacteriophage lambda major capsid protein mutant - W308A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7sj5
TitleBacteriophage lambda major capsid protein mutant - W308A
ComponentsMajor capsid protein
KeywordsSTRUCTURAL PROTEIN / major capsid protein / HK97-fold / assembly incompetent
Function / homology
Function and homology information


T=7 icosahedral viral capsid / viral capsid / host cell cytoplasm
Similarity search - Function
capsid protein of prophage fold / capsid protein of prophage domain / Major capsid protein GpE / Phage major capsid protein E / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Major capsid protein
Similarity search - Component
Biological speciesEscherichia phage lambda (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.695 Å
AuthorsDavis, C.R. / Churchill, M.E.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB 2016019 United States
National Science Foundation (NSF, United States)GRFP 2016218284 United States
CitationJournal: J.Mol.Biol. / Year: 2022
Title: Characterization of a Primordial Major Capsid-Scaffolding Protein Complex in Icosahedral Virus Shell Assembly.
Authors: Davis, C.R. / Backos, D. / Morais, M.C. / Churchill, M.E.A. / Catalano, C.E.
History
DepositionOct 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein


Theoretical massNumber of molelcules
Total (without water)152,4564
Polymers152,4564
Non-polymers00
Water2,936163
1
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein

D: Major capsid protein


Theoretical massNumber of molelcules
Total (without water)152,4564
Polymers152,4564
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_548-x+1/2,y-1/2,-z+31
Buried area8470 Å2
ΔGint-18 kcal/mol
Surface area60420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.153, 95.303, 113.121
Angle α, β, γ (deg.)90.000, 127.920, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

#1: Protein
Major capsid protein / Gene product E / gpE / Major head protein


Mass: 38114.027 Da / Num. of mol.: 4 / Mutation: W308A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage lambda (virus) / Gene: E, lambdap08, gpE / Production host: Escherichia coli (E. coli) / References: UniProt: P03713
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.37 Å3/Da / Density % sol: 48.17 % / Description: 70 micron rhomboid prism
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 0.1 M bis-tris, 0.1 M ammonium sulfate, 5% v/v glycerol, 30% v/v PEG-3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Sep 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.695→29.75 Å / Num. obs: 39376 / % possible obs: 99.53 % / Redundancy: 3.7 % / Biso Wilson estimate: 49.19 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.05594 / Rpim(I) all: 0.0336 / Rrim(I) all: 0.06535 / Net I/av σ(I): 18.27 / Net I/σ(I): 18.27
Reflection shellResolution: 2.695→2.791 Å / Num. unique obs: 3819 / CC1/2: 0.919

-
Processing

Software
NameVersionClassification
PHENIXdev-3724refinement
XDSdata reduction
pointlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BQW

3bqw


Resolution: 2.695→29.75 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2295 2044 -
Rwork0.2074 --
obs-39363 99.53 %
Displacement parametersBiso mean: 74.44 Å2
Refinement stepCycle: LAST / Resolution: 2.695→29.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10638 0 0 163 10801
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210842
X-RAY DIFFRACTIONf_angle_d0.456814679
X-RAY DIFFRACTIONf_chiral_restr0.04111616
X-RAY DIFFRACTIONf_plane_restr0.00361941
X-RAY DIFFRACTIONf_dihedral_angle_d15.97724096
LS refinement shellResolution: 2.695→2.791 Å
RfactorNum. reflection% reflection
Rfree0.3087 195 -
Rwork0.2739 3819 -
obs--97.15 %

+
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