[English] 日本語
Yorodumi
- PDB-6vpa: Scabin (N110A) toxin from Streptomyces scabies -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vpa
TitleScabin (N110A) toxin from Streptomyces scabies
ComponentsScabin
KeywordsTOXIN / Transferase
Function / homology: / : / Scabin-like / nucleotide binding / Putative secreted protein
Function and homology information
Biological speciesStreptomyces scabiei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLyons, B. / Lidster, T. / Merrill, A.R.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Toxins / Year: 2021
Title: Mapping the DNA-Binding Motif of Scabin Toxin, a Guanine Modifying Enzyme from Streptomyces scabies .
Authors: Vatta, M. / Lyons, B. / Heney, K.A. / Lidster, T. / Merrill, A.R.
History
DepositionFeb 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.title / _citation.year
Revision 1.2Jan 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Oct 11, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Scabin


Theoretical massNumber of molelcules
Total (without water)21,8141
Polymers21,8141
Non-polymers00
Water2,216123
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8410 Å2
Unit cell
Length a, b, c (Å)88.370, 60.730, 37.910
Angle α, β, γ (deg.)90.000, 99.430, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-333-

HOH

21A-370-

HOH

31A-415-

HOH

-
Components

#1: Protein Scabin


Mass: 21814.145 Da / Num. of mol.: 1 / Fragment: UNP residues 29-200 / Mutation: N110A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces scabiei (strain 87.22) (bacteria)
Strain: 87.22 / Gene: SCAB_27771 / Production host: Escherichia coli (E. coli) / References: UniProt: C9Z6T8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 46.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 14% PEG400, 0.1 M MES, pH 6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.979 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Dec 13, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.5→43.59 Å / Num. obs: 31488 / % possible obs: 99 % / Redundancy: 4.5 % / Biso Wilson estimate: 18.28 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.0424 / Rpim(I) all: 0.02301 / Rrim(I) all: 0.04839 / Net I/σ(I): 20.16
Reflection shellResolution: 1.5→1.554 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.3464 / Mean I/σ(I) obs: 3.79 / Num. unique obs: 2954 / CC1/2: 0.925 / CC star: 0.98 / Rpim(I) all: 0.1989 / Rrim(I) all: 0.4019 / % possible all: 93

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
PDB_EXTRACT3.25data extraction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5DAZ

5daz


Resolution: 1.5→43.588 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1715 1573 5 %
Rwork0.1439 29907 -
obs0.1453 31480 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.02 Å2 / Biso mean: 28.1323 Å2 / Biso min: 12.12 Å2
Refinement stepCycle: final / Resolution: 1.5→43.588 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1251 0 0 123 1374
Biso mean---37.06 -
Num. residues----163
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5-1.54840.20781330.164252192
1.5484-1.60380.18521420.13552710100
1.6038-1.6680.17321450.12582768100
1.668-1.74390.15641430.12262727100
1.7439-1.83580.18561420.11792705100
1.8358-1.95090.14931430.11742710100
1.9509-2.10150.15991450.12452757100
2.1015-2.31290.17021430.13322724100
2.3129-2.64760.15471450.13932745100
2.6476-3.33550.17841440.15822744100
3.3355-43.580.1781480.15842796100

+
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