[English] 日本語
Yorodumi
- PDB-6bff: Structure of the aminoglycoside acetyltransferase AAC(6')-Im -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6bff
TitleStructure of the aminoglycoside acetyltransferase AAC(6')-Im
ComponentsAminoglycoside acetyltransferase
KeywordsTRANSFERASE / antibiotic resistance / aminoglycoside / acetyltransferase
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups / response to antibiotic / metal ion binding
Similarity search - Function
Acetyltransferase (GNAT) domain / 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
Aminoglycoside acetyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSmith, C.A. / Vakulenko, S.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI057393 United States
CitationJournal: Microb Cell / Year: 2017
Title: Aminoglycoside resistance profile and structural architecture of the aminoglycoside acetyltransferase AAC(6')-Im.
Authors: Smith, C.A. / Bhattacharya, M. / Toth, M. / Stewart, N.K. / Vakulenko, S.B.
History
DepositionOct 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 27, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aminoglycoside acetyltransferase
B: Aminoglycoside acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2564
Polymers43,2072
Non-polymers492
Water4,918273
1
A: Aminoglycoside acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6282
Polymers21,6041
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Aminoglycoside acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6282
Polymers21,6041
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)161.550, 34.950, 67.320
Angle α, β, γ (deg.)90.000, 102.330, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-427-

HOH

21B-432-

HOH

31B-434-

HOH

-
Components

#1: Protein Aminoglycoside acetyltransferase


Mass: 21603.604 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: aac(6')-Im / Production host: Escherichia coli (E. coli) / References: UniProt: Q93ET8
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.15 Å3/Da / Density % sol: 42.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M MgCl2, 0.1 M Tris HCl pH 8.5, 30% PEG 4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→39.6 Å / Num. obs: 39826 / % possible obs: 96.9 % / Redundancy: 3.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.061 / Net I/σ(I): 12.9
Reflection shellResolution: 1.7→1.75 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2771 / CC1/2: 0.784 / % possible all: 91.8

-
Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QC6

4qc6


Resolution: 1.7→34.123 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.43
RfactorNum. reflection% reflection
Rfree0.2293 2012 5.05 %
Rwork0.1846 --
obs0.1868 39826 97.07 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 87.83 Å2 / Biso mean: 28.0345 Å2 / Biso min: 9.14 Å2
Refinement stepCycle: final / Resolution: 1.7→34.123 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3034 0 2 275 3311
Biso mean--25.9 33.73 -
Num. residues----356
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083123
X-RAY DIFFRACTIONf_angle_d0.9314195
X-RAY DIFFRACTIONf_chiral_restr0.062429
X-RAY DIFFRACTIONf_plane_restr0.006542
X-RAY DIFFRACTIONf_dihedral_angle_d15.471881
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.74250.42811370.34532589272694
1.7425-1.78970.32851240.3182657278196
1.7897-1.84230.34181460.2612627277395
1.8423-1.90180.26821620.23042662282497
1.9018-1.96970.22951520.19082675282798
1.9697-2.04860.22921490.18352743289298
2.0486-2.14180.22531330.17582664279798
2.1418-2.25470.22181390.17982693283297
2.2547-2.3960.28051380.18562739287799
2.396-2.58090.23171540.18992728288298
2.5809-2.84050.21331450.18722678282395
2.8405-3.25120.23761330.18512764289799
3.2512-4.09510.18991530.15742723287697
4.0951-34.13010.2091470.16732872301998
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)
12.65430.02350.24453.03280.23462.1065-0.0184-0.10990.04270.173-0.03170.055-0.0663-0.09890.04920.10310.0177-0.01890.1231-0.00830.09666.3377-0.45385.6102
24.87091.50830.13540.93690.08530.02890.1856-0.67810.35260.4528-0.25610.1304-0.587-0.38550.07120.44320.06670.01460.5114-0.05190.31616.5158.02817.6623
32.8272-0.16041.36291.13730.25431.9585-0.0775-0.01970.11280.0453-0.0286-0.0911-0.10460.07480.10450.1604-0.00450.02150.13850.01660.134819.31351.91428.8076
42.5168-0.6141-0.69781.7414-0.39663.1389-0.0172-0.1331-0.28060.0556-0.0126-0.05060.2022-0.050.05270.14-0.0102-0.0080.17210.02450.169522.2549-8.728413.9534
51.8699-0.08360.30761.89980.21991.650.13890.1628-0.1496-0.1466-0.2004-0.01040.06430.1390.04820.17320.04940.00110.17860.01190.16164.87341.224524.5324
64.38931.76183.51750.76941.5162.98770.5283-0.7844-0.71960.2042-0.20290.36330.8919-0.5154-0.44380.4065-0.0141-0.00150.33680.16620.524257.9484-8.020432.7661
73.3077-0.07780.47162.1102-0.3531.76530.10370.1525-0.38-0.1455-0.12650.14640.118-0.0230.01670.15990.0188-0.00880.1003-0.02310.149852.5343-1.078518.8131
82.544-0.53230.38152.1054-0.02333.0624-0.0186-0.04030.2524-0.0165-0.08910.0921-0.1766-0.0950.10680.14660.0053-0.00520.1779-0.00520.185247.09389.257822.3426
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 41 )A1 - 41
2X-RAY DIFFRACTION2chain 'A' and (resid 42 through 56 )A42 - 56
3X-RAY DIFFRACTION3chain 'A' and (resid 57 through 140 )A57 - 140
4X-RAY DIFFRACTION4chain 'A' and (resid 141 through 178 )A141 - 178
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 41 )B2 - 41
6X-RAY DIFFRACTION6chain 'B' and (resid 42 through 56 )B42 - 56
7X-RAY DIFFRACTION7chain 'B' and (resid 57 through 140 )B57 - 140
8X-RAY DIFFRACTION8chain 'B' and (resid 141 through 178 )B141 - 178

+
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