[English] 日本語
Yorodumi
- PDB-8twg: Crystal structure of tetracycline destructase Tet(56-2) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8twg
TitleCrystal structure of tetracycline destructase Tet(56-2)
Components6-hydroxynicotinate 3-monooxygenase
KeywordsOXIDOREDUCTASE
Function / homology6-hydroxynicotinate 3-monooxygenase / 6-hydroxynicotinate 3-monooxygenase activity / : / FAD-binding domain / FAD binding domain / FAD binding / FAD/NAD(P)-binding domain superfamily / FLAVIN-ADENINE DINUCLEOTIDE / 6-hydroxynicotinate 3-monooxygenase
Function and homology information
Biological speciesLegionella clemsonensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKumar, H. / Tang, W.K. / Tolia, N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Commun Biol / Year: 2024
Title: Sequence-structure-function characterization of the emerging tetracycline destructase family of antibiotic resistance enzymes.
Authors: Blake, K.S. / Kumar, H. / Loganathan, A. / Williford, E.E. / Diorio-Toth, L. / Xue, Y.P. / Tang, W.K. / Campbell, T.P. / Chong, D.D. / Angtuaco, S. / Wencewicz, T.A. / Tolia, N.H. / Dantas, G.
History
DepositionAug 21, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: 6-hydroxynicotinate 3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3882
Polymers45,6031
Non-polymers7861
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.790, 70.548, 128.314
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

-
Components

#1: Protein 6-hydroxynicotinate 3-monooxygenase


Mass: 45602.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella clemsonensis (bacteria) / Gene: clem_00015 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A222NYA8
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.15 M Magnesium formate, 15% Polyethylene glycol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.8→19.97 Å / Num. obs: 40189 / % possible obs: 99.82 % / Redundancy: 6.51 % / Biso Wilson estimate: 22.73 Å2 / CC1/2: 0.99 / Net I/σ(I): 17.78
Reflection shellResolution: 1.8→1.86 Å / Num. unique obs: 3916 / CC1/2: 0.93

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→19.97 Å / SU ML: 0.1826 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.1046
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2095 1998 4.97 %
Rwork0.1744 38190 -
obs0.1761 40188 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.86 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3073 0 53 259 3385
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00893191
X-RAY DIFFRACTIONf_angle_d0.87744313
X-RAY DIFFRACTIONf_chiral_restr0.0542466
X-RAY DIFFRACTIONf_plane_restr0.0081552
X-RAY DIFFRACTIONf_dihedral_angle_d14.21421167
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.31381360.25012600X-RAY DIFFRACTION97.71
1.84-1.890.25141420.21522708X-RAY DIFFRACTION99.96
1.89-1.950.22081400.19442705X-RAY DIFFRACTION99.89
1.95-2.010.20981400.18472676X-RAY DIFFRACTION99.75
2.01-2.080.23181400.1872679X-RAY DIFFRACTION100
2.08-2.170.24771430.1882719X-RAY DIFFRACTION99.93
2.17-2.270.22551410.17162693X-RAY DIFFRACTION100
2.27-2.380.22431420.1712721X-RAY DIFFRACTION100
2.38-2.530.21241420.17472709X-RAY DIFFRACTION99.96
2.53-2.730.2491450.18112770X-RAY DIFFRACTION100
2.73-30.22161420.18462725X-RAY DIFFRACTION100
3-3.440.19051450.17862754X-RAY DIFFRACTION100
3.44-4.320.18211460.15042803X-RAY DIFFRACTION100
4.32-19.970.18711540.16362928X-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