[English] 日本語
Yorodumi
- PDB-5tlb: Scabin toxin from Streptomyces scabies in complex with NADH -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5tlb
TitleScabin toxin from Streptomyces scabies in complex with NADH
ComponentsScabin
KeywordsTRANSFERASE / TOXIN / inhibitor
Function / homology: / Scabin-like / nucleotide binding / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Putative secreted protein
Function and homology information
Biological speciesStreptomyces scabiei 87.22 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLyons, B. / Dutta, D. / Ravulapalli, R. / Merrill, A.R.
CitationJournal: Biochem. J. / Year: 2018
Title: Characterization of the catalytic signature of Scabin toxin, a DNA-targeting ADP-ribosyltransferase.
Authors: Lyons, B. / Lugo, M.R. / Carlin, S. / Lidster, T. / Merrill, A.R.
History
DepositionOct 10, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2017Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Oct 4, 2023Group: 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: Scabin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6582
Polymers21,9931
Non-polymers6651
Water2,486138
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-5 kcal/mol
Surface area8520 Å2
Unit cell
Length a, b, c (Å)86.040, 62.260, 38.080
Angle α, β, γ (deg.)90.000, 100.300, 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 on special symmetry positions
IDModelComponents
11A-495-

HOH

-
Components

#1: Protein Scabin


Mass: 21992.600 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces scabiei 87.22 (bacteria) / Strain: 87.22 / Gene: SCAB_27771 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: C9Z6T8, NAD+-protein-arginine ADP-ribosyltransferase
#2: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.28 Å3/Da / Density % sol: 46.09 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM potassium chloride, 50 mM sodium cacodylate trihydrate, pH 6.0, 16% PEG1000, 0.5 mM spermine

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 11, 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: 1.7→42.34 Å / Num. obs: 21771 / % possible obs: 99.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 25.14 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.031 / Rsym value: 0.06 / Net I/σ(I): 15.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRsym value% possible all
1.7-1.763.70.7651.821580.7160.4610.89599.8
1.76-1.833.80.4952.721880.8760.2960.57899.7
1.83-1.914.10.3174.121420.9460.190.3799.7
1.91-2.023.80.1974.121700.9740.1180.23199.6
2.02-2.143.80.14921730.9880.0840.16399.7
2.14-2.313.80.112.521580.9920.060.11799.7
2.31-2.543.80.07316.621850.9950.0430.08599.6
2.54-2.913.80.0482421860.9970.0290.05699.9
2.91-3.663.80.03234.421780.9980.0190.03899.9
3.66-42.343.80.02741.722330.9980.0160.03199.6

-
Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5DAZ

5daz


Resolution: 1.7→42.34 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.1961 1087 5 %
Rwork0.1592 --
obs-21771 -
Displacement parametersBiso mean: 32.82 Å2
Refinement stepCycle: LAST / Resolution: 1.7→42.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1275 0 44 139 1458
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_angle_d0.8331898
X-RAY DIFFRACTIONf_bond_d0.0061374
X-RAY DIFFRACTIONf_chiral_restr0.051201
X-RAY DIFFRACTIONf_dihedral_angle_d15.702792
X-RAY DIFFRACTIONf_plane_restr0.005246
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / % reflection Rfree: 5 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7-1.780.28761340.2528256699.6
1.78-1.870.29511340.1939256099.6
1.87-1.990.20371350.1746255599.5
1.99-2.140.23351370.1641259499.6
2.14-2.360.22461340.1513255899.6
2.36-2.70.19451370.1524260199.7
2.7-3.40.18261360.1585258899.9
3.4-42.340.16981400.1482264199.6

+
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