[English] 日本語
Yorodumi
- PDB-7lxs: Structural and Biochemical Insight into Assembly of Molecular Mot... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7lxs
TitleStructural and Biochemical Insight into Assembly of Molecular Motors Involved in Viral DNA Packaging
ComponentsTerminase, small subunit
KeywordsVIRAL PROTEIN / DNA Packaging / Terminase
Biological speciesBacteriophage sp. (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsOrtega, M.E.
CitationJournal: To Be Published
Title: Structural and Biochemical Insight into Assembly of Molecular Motors Involved in Viral DNA Packaging
Authors: Ortega, M.E. / Randriamihaja, A. / Rossen, N. / Brannon, J.P. / Marquez, C. / West, R. / Dabbagh, S. / Robles, R. / LeGue, A.
History
DepositionMar 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 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: Terminase, small subunit
B: Terminase, small subunit
C: Terminase, small subunit
D: Terminase, small subunit
E: Terminase, small subunit
F: Terminase, small subunit
G: Terminase, small subunit
H: Terminase, small subunit


Theoretical massNumber of molelcules
Total (without water)47,0298
Polymers47,0298
Non-polymers00
Water00
1
A: Terminase, small subunit
C: Terminase, small subunit


Theoretical massNumber of molelcules
Total (without water)11,7572
Polymers11,7572
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-13 kcal/mol
Surface area5520 Å2
MethodPISA
2
B: Terminase, small subunit

D: Terminase, small subunit


Theoretical massNumber of molelcules
Total (without water)11,7572
Polymers11,7572
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area1140 Å2
ΔGint-12 kcal/mol
Surface area5570 Å2
MethodPISA
3
E: Terminase, small subunit
H: Terminase, small subunit


Theoretical massNumber of molelcules
Total (without water)11,7572
Polymers11,7572
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-12 kcal/mol
Surface area5540 Å2
MethodPISA
4
F: Terminase, small subunit

G: Terminase, small subunit


Theoretical massNumber of molelcules
Total (without water)11,7572
Polymers11,7572
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area1140 Å2
ΔGint-12 kcal/mol
Surface area5570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.747, 50.761, 68.527
Angle α, β, γ (deg.)90.000, 88.360, 90.110
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Terminase, small subunit


Mass: 5878.606 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteriophage sp. (virus) / Production host: Escherichia coli (E. coli)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.83 Å3/Da / Density % sol: 32.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: 50mM MES pH 6.5, 10mM zinc chloride, 20% PEG 400

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5 Å
DetectorType: RIGAKU HyPix-3000 / Detector: PIXEL / Date: Aug 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2.206→24.74 Å / Num. obs: 15881 / % possible obs: 95.1 % / Redundancy: 3.7 % / CC1/2: 0.999 / Net I/σ(I): 93.9
Reflection shellResolution: 2.21→2.29 Å / Num. unique obs: 1287 / CC1/2: 0.999

-
Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7LW0

7lw0


Resolution: 2.21→24.74 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.952 / SU B: 0.009 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.156 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.142 1605 10.1 %RANDOM
Rwork0.1398 ---
obs0.14 14295 94.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 51.92 Å2 / Biso mean: 18.288 Å2 / Biso min: 6.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.03 Å2-0.01 Å2
2---0.03 Å2-0.02 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.21→24.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3296 0 0 0 3296
Num. residues----440
LS refinement shellResolution: 2.21→2.263 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.254 93 -
Rwork0.253 900 -
obs--78.19 %

+
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