[English] 日本語
Yorodumi
- PDB-5f46: Crystal structure of an aminoglycoside acetyltransferase meta-AAC... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5f46
TitleCrystal structure of an aminoglycoside acetyltransferase meta-AAC0020 from an uncultured soil metagenomic sample, apoenzyme form
Componentsaminoglycoside acetyltransferase meta-AAC0020
KeywordsTRANSFERASE / GNAT fold / GCN5-N-acetyltransferase fold / acetyltransferase / aminoglycoside / antibiotic resistance / metagenome / soil / coenzyme A / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups / metal ion binding
Similarity search - Function
Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsXu, Z. / Skarina, T. / Stogios, P.J. / Yim, V. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: ACS Infect Dis / Year: 2017
Title: Structural and Functional Survey of Environmental Aminoglycoside Acetyltransferases Reveals Functionality of Resistance Enzymes.
Authors: Xu, Z. / Stogios, P.J. / Quaile, A.T. / Forsberg, K.J. / Patel, S. / Skarina, T. / Houliston, S. / Arrowsmith, C. / Dantas, G. / Savchenko, A.
History
DepositionDec 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2016Group: Structure summary
Revision 1.2Apr 3, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / pdbx_database_related / pdbx_struct_oper_list / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.pdbx_description / _pdbx_struct_oper_list.symmetry_operation / _struct.pdbx_descriptor / _struct.title
Revision 1.3Sep 27, 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 acetyltransferase meta-AAC0020
B: aminoglycoside acetyltransferase meta-AAC0020
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1254
Polymers37,0542
Non-polymers712
Water6,377354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6280 Å2
ΔGint-52 kcal/mol
Surface area15070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.850, 61.807, 114.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein aminoglycoside acetyltransferase meta-AAC0020


Mass: 18526.986 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A059WZ16
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 354 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 4 M sodium formate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 33193 / % possible obs: 97.2 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 0.577
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.405 / % possible all: 97.1

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YFJ

4yfj


Resolution: 1.85→29.842 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2526 1592 4.99 %Random selection
Rwork0.2086 ---
obs0.2107 31885 93.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→29.842 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2522 0 2 354 2878
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042605
X-RAY DIFFRACTIONf_angle_d0.7813533
X-RAY DIFFRACTIONf_dihedral_angle_d14.16961
X-RAY DIFFRACTIONf_chiral_restr0.033383
X-RAY DIFFRACTIONf_plane_restr0.004454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8493-1.9090.30191270.27832479X-RAY DIFFRACTION86
1.909-1.97720.28341340.25042562X-RAY DIFFRACTION88
1.9772-2.05630.22711370.23322648X-RAY DIFFRACTION91
2.0563-2.14990.26351420.22272643X-RAY DIFFRACTION92
2.1499-2.26320.26691400.22932705X-RAY DIFFRACTION93
2.2632-2.4050.28441450.22742730X-RAY DIFFRACTION93
2.405-2.59060.28191490.23822768X-RAY DIFFRACTION94
2.5906-2.85110.29041500.24652855X-RAY DIFFRACTION97
2.8511-3.26320.29691530.21932943X-RAY DIFFRACTION99
3.2632-4.10960.20991540.1742908X-RAY DIFFRACTION97
4.1096-29.84560.23291610.18953052X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.39245.5585-5.84074.7907-3.91896.23420.18430.96640.2636-0.12160.556-0.506-2.0919-0.5772-0.71811.2563-0.14290.18010.5166-0.0690.540236.877150.22478.2631
21.61530.1115-0.3832.5879-0.19087.2913-0.00050.2226-0.0467-0.40410.0960.0054-0.27720.0178-0.09040.2842-0.01310.01720.2231-0.02910.250534.266134.630614.8031
32.5141-2.1832-0.24371.910.51735.39240.14820.23890.2687-0.42260.0822-0.47-0.85920.8362-0.15740.5571-0.24750.0820.4702-0.07380.341444.566642.663413.5841
41.4178-0.3249-0.46333.35120.46121.0033-0.04990.03020.1435-0.51420.4097-0.9209-0.17110.5121-0.30570.3297-0.11120.08480.4897-0.18030.423946.434837.673124.6979
59.7754.8021-3.11835.0491-4.53524.54080.7156-0.6264-1.882-0.0315-1.0522-0.45782.21030.8410.35321.00580.0931-0.13310.51410.06750.704936.245511.716848.26
65.1846-0.11811.43155.6598-0.63573.76870.0701-0.34580.29460.8137-0.04610.2242-0.1730.0592-0.02960.3820.03820.05650.257-0.0340.180631.314429.656843.3138
71.0390.36181.51742.8218-2.82056.2960.009-0.0665-0.01380.1878-0.0362-0.20740.43060.39390.0270.3620.1393-0.01650.3347-0.04460.309139.020922.138936.0288
81.4843-0.73090.44553.2293-0.09151.0985-0.0952-0.01330.0650.5080.3646-1.06360.09960.6263-0.23470.33290.1072-0.07660.5452-0.18060.510346.249526.395531.0359
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 8:15)
2X-RAY DIFFRACTION2(chain A and resid 16:86)
3X-RAY DIFFRACTION3(chain A and resid 87:111)
4X-RAY DIFFRACTION4(chain A and resid 112:157)
5X-RAY DIFFRACTION5(chain B and resid 7:14)
6X-RAY DIFFRACTION6(chain B and resid 15:65)
7X-RAY DIFFRACTION7(chain B and resid 66:113)
8X-RAY DIFFRACTION8(chain B and resid 114:157)

+
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