[English] 日本語
Yorodumi
- PDB-6vr3: Aminoglycoside N-2'-Acetyltransferase-Ia [AAC(2')-Ia] in complex ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vr3
TitleAminoglycoside N-2'-Acetyltransferase-Ia [AAC(2')-Ia] in complex with acetylated-netilmicin and CoA
ComponentsAminoglycoside 2'-N-acetyltransferase
KeywordsTRANSFERASE / Acetyltransferase / GNAT superfamily
Function / homology
Function and homology information


gentamicin 2'-N-acetyltransferase / aminoglycoside 2'-N-acetyltransferase activity / response to antibiotic
Similarity search - Function
Acetyltransferase (GNAT) domain / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
COENZYME A / Chem-NTL / Aminoglycoside 2'-N-acetyltransferase
Similarity search - Component
Biological speciesProvidencia stuartii (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsBassenden, A.V. / Berghuis, A.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-162365 Canada
CitationJournal: Sci Rep / Year: 2021
Title: Structural and phylogenetic analyses of resistance to next-generation aminoglycosides conferred by AAC(2') enzymes.
Authors: Bassenden, A.V. / Dumalo, L. / Park, J. / Blanchet, J. / Maiti, K. / Arya, D.P. / Berghuis, A.M.
History
DepositionFeb 6, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 11, 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: Aminoglycoside 2'-N-acetyltransferase
B: Aminoglycoside 2'-N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0646
Polymers40,4942
Non-polymers2,5704
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-11 kcal/mol
Surface area16500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.038, 73.038, 145.550
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Aminoglycoside 2'-N-acetyltransferase / AAC(2')-Ia


Mass: 20246.842 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Providencia stuartii (bacteria) / Gene: aac / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q52424, gentamicin 2'-N-acetyltransferase
#2: Chemical ChemComp-NTL / N-[(2S,3R)-2-{[(1R,2S,3S,4R,6S)-6-amino-3-{[3-deoxy-4-C-methyl-3-(methylamino)-beta-L-lyxopyranosyl]oxy}-4-(ethylamino) -2-hydroxycyclohexyl]oxy}-6-(aminomethyl)-3,4-dihydro-2H-pyran-3-yl]acetamide / acetylated-netilmicin


Mass: 517.616 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H43N5O8 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.77 Å3/Da / Density % sol: 55.56 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: NaSCN, MPD, Acetyl CoA, Netilmicin

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Feb 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34 Å / Relative weight: 1
ReflectionResolution: 2→26.49 Å / Num. obs: 58685 / % possible obs: 99.92 % / Redundancy: 2 % / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 20.82
Reflection shellResolution: 2→2.071 Å / Num. unique obs: 3059 / CC1/2: 0.761 / CC star: 0.913

-
Processing

Software
NameVersionClassification
PHENIX(1.17_3644: ???)refinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6VR2

6vr2


Resolution: 2→26.49 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.14
RfactorNum. reflection% reflection
Rfree0.226 3770 6.42 %
Rwork0.1805 --
obs0.1834 58685 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→26.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2746 0 168 170 3084
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083050
X-RAY DIFFRACTIONf_angle_d0.8664147
X-RAY DIFFRACTIONf_dihedral_angle_d31.3381061
X-RAY DIFFRACTIONf_chiral_restr0.052441
X-RAY DIFFRACTIONf_plane_restr0.004515
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.35191480.31662061X-RAY DIFFRACTION100
2.03-2.050.34291280.29862005X-RAY DIFFRACTION99
2.05-2.080.31451460.27272047X-RAY DIFFRACTION100
2.08-2.110.30531350.26342006X-RAY DIFFRACTION100
2.11-2.140.30011440.24452089X-RAY DIFFRACTION100
2.14-2.170.26151440.23762016X-RAY DIFFRACTION100
2.17-2.210.29481380.22342026X-RAY DIFFRACTION100
2.21-2.250.26271380.22381998X-RAY DIFFRACTION100
2.25-2.290.30951460.21642075X-RAY DIFFRACTION100
2.29-2.330.24681300.20522013X-RAY DIFFRACTION100
2.33-2.380.23631410.19832032X-RAY DIFFRACTION100
2.38-2.430.26691420.18632069X-RAY DIFFRACTION100
2.43-2.490.29021420.20841971X-RAY DIFFRACTION100
2.49-2.550.24941380.19922063X-RAY DIFFRACTION100
2.55-2.620.25541380.18982007X-RAY DIFFRACTION100
2.62-2.70.25851380.19632064X-RAY DIFFRACTION100
2.7-2.780.29261400.19522045X-RAY DIFFRACTION100
2.78-2.880.24771240.18032034X-RAY DIFFRACTION100
2.88-30.21641400.17122010X-RAY DIFFRACTION100
3-3.140.19181380.16932038X-RAY DIFFRACTION100
3.14-3.30.17991420.16062052X-RAY DIFFRACTION100
3.3-3.510.19021380.15432056X-RAY DIFFRACTION100
3.51-3.780.18381460.14411991X-RAY DIFFRACTION100
3.78-4.150.18321410.13472027X-RAY DIFFRACTION100
4.16-4.750.1591400.12812031X-RAY DIFFRACTION100
4.75-5.980.16671450.16332050X-RAY DIFFRACTION100
5.98-26.490.25111400.17822039X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 59.3731 Å / Origin y: 30.4961 Å / Origin z: 164.8221 Å
111213212223313233
T0.1446 Å2-0.0088 Å20.0004 Å2-0.1465 Å20.0118 Å2--0.1243 Å2
L1.7161 °2-0.1581 °2-0.0638 °2-2.0935 °2-0.0451 °2--0.7549 °2
S0.084 Å °0.0345 Å °0.064 Å °0.1214 Å °-0.0686 Å °-0.0629 Å °-0.0133 Å °-0.0495 Å °-0.0129 Å °
Refinement TLS groupSelection details: all

+
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