[English] 日本語
Yorodumi
- PDB-4evy: Crystal structure of aminoglycoside antibiotic 6'-N-acetyltransfe... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4evy
TitleCrystal structure of aminoglycoside antibiotic 6'-N-acetyltransferase AAC(6')-Ig from Acinetobacter haemolyticus in complex with tobramycin
ComponentsAminoglycoside N(6')-acetyltransferase type 1
KeywordsTRANSFERASE/ANTIBIOTIC / Center for Structural Genomics of Infectious Diseases (CSGID) / NIAID / National Institute of Allergy and Infectious Diseases / GNAT superfamily / GCN5-related N-acetyltransferase superfamily / N-acetyltransferase fold / antibiotic resistance / acetyl coenzyme A / intracellular / TRANSFERASE-ANTIBIOTIC complex
Function / homology
Function and homology information


aminoglycoside 6'-N-acetyltransferase / aminoglycoside 6'-N-acetyltransferase activity / response to antibiotic
Similarity search - Function
Aminoglycoside N6-acetyltransferase / 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
: / TOBRAMYCIN / Aminoglycoside N(6')-acetyltransferase type 1
Similarity search - Component
Biological speciesAcinetobacter haemolyticus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.768 Å
AuthorsStogios, P.J. / Evdokimova, E. / Minasov, G. / Yim, V. / Courvalin, P. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: ACS Infect Dis. / Year: 2017
Title: Structural and Biochemical Characterization of Acinetobacter spp. Aminoglycoside Acetyltransferases Highlights Functional and Evolutionary Variation among Antibiotic Resistance Enzymes.
Authors: Stogios, P.J. / Kuhn, M.L. / Evdokimova, E. / Law, M. / Courvalin, P. / Savchenko, A.
History
DepositionApr 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2016Group: Database references
Revision 1.2Feb 22, 2017Group: Database references
Revision 1.3Sep 13, 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 / struct_ref_seq_dif / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aminoglycoside N(6')-acetyltransferase type 1
B: Aminoglycoside N(6')-acetyltransferase type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9189
Polymers37,7992
Non-polymers1,1207
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6550 Å2
ΔGint-61 kcal/mol
Surface area14770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.723, 43.789, 46.282
Angle α, β, γ (deg.)83.65, 87.49, 68.41
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Aminoglycoside N(6')-acetyltransferase type 1 / AAC(6')-Ig / Aminoglycoside resistance protein


Mass: 18899.291 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter haemolyticus (bacteria) / Strain: BM2685 / Gene: aac(6')-Ig / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q44057, aminoglycoside 6'-N-acetyltransferase
#2: Chemical ChemComp-TOY / TOBRAMYCIN / 4-AMINO-2-[4,6-DIAMINO-3-(3-AMINO-6-AMINOMETHYL-5-HYDROXY-TETRAHYDRO-PYRAN-2-YLOXY)-2-HYDROXY-CYCLOHEXYLOXY]-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-3,5-DIOL


Mass: 467.514 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H37N5O9 / Comment: antibiotic*YM
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 223 / 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: 1.97 Å3/Da / Density % sol: 37.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.05 M magnesium chloride, 25% PEG3350, 0.05 M trisodium citrate dihydrate, pH 4.6, 5 mM tobramicin, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 5, 2012
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.768→30 Å / Num. all: 28099 / Num. obs: 26273 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rsym value: 0.051 / Net I/σ(I): 40.79
Reflection shellResolution: 1.768→1.8 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.91 / Rsym value: 0.658 / % possible all: 87.3

-
Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIX(phenix.phaser)model building
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1S3Z

1s3z


Resolution: 1.768→28.971 Å / SU ML: 0.28 / σ(F): 1.96 / Phase error: 23.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2134 1245 5 %
Rwork0.1669 --
obs0.1692 25205 91.87 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.352 Å2 / ksol: 0.375 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.0773 Å2-3.2265 Å2-1.4358 Å2
2---1.5335 Å22.0132 Å2
3----2.5438 Å2
Refinement stepCycle: LAST / Resolution: 1.768→28.971 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2329 0 69 223 2621
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122503
X-RAY DIFFRACTIONf_angle_d1.3563396
X-RAY DIFFRACTIONf_dihedral_angle_d15.41939
X-RAY DIFFRACTIONf_chiral_restr0.099391
X-RAY DIFFRACTIONf_plane_restr0.006422
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.768-1.8020.35941290.34692478X-RAY DIFFRACTION82
1.802-1.83870.34581380.32342620X-RAY DIFFRACTION90
1.8387-1.87870.30671480.29642757X-RAY DIFFRACTION91
1.8787-1.92240.31231400.25012667X-RAY DIFFRACTION91
1.9224-1.97050.30221440.22452745X-RAY DIFFRACTION92
1.9705-2.02370.28491410.19152678X-RAY DIFFRACTION91
2.0237-2.08330.23651470.17992811X-RAY DIFFRACTION92
2.0833-2.15050.25991440.16292725X-RAY DIFFRACTION92
2.1505-2.22730.18161420.17372772X-RAY DIFFRACTION93
2.2273-2.31650.2831460.16582747X-RAY DIFFRACTION93
2.3165-2.42180.2411460.18172785X-RAY DIFFRACTION94
2.4218-2.54940.23741470.17112783X-RAY DIFFRACTION94
2.5494-2.70910.2521480.18932790X-RAY DIFFRACTION94
2.7091-2.91810.27181460.18142785X-RAY DIFFRACTION93
2.9181-3.21140.23961410.16572715X-RAY DIFFRACTION93
3.2114-3.67530.17541470.1462739X-RAY DIFFRACTION91
3.6753-4.62740.13571490.12332825X-RAY DIFFRACTION94
4.6274-28.97520.17631450.14392799X-RAY DIFFRACTION94
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)
17.61010.5001-0.13845.6677-1.30755.76710.10690.2171-0.2134-0.0803-0.3871-0.36540.53830.86960.20520.21950.034-0.0510.14930.04410.1743-6.34125.6520.6989
21.59440.27120.16813.65640.17942.9862-0.00970.1628-0.0617-0.26920.00730.18780.1632-0.0326-0.00190.1076-0-0.02580.1230.00350.1003-14.11918.5922-2.3978
35.9245-2.00321.25712.2622-0.7138.5795-0.2062-0.58160.11210.42460.25780.3498-0.649-0.5884-0.01280.2630.02620.05360.2246-0.010.221-23.180937.74620.6829
41.96420.5599-0.2522.4359-0.06663.30020.0474-0.18750.17650.2135-0.0382-0.0239-0.32440.19680.00880.1875-0.018-0.00810.1375-0.00780.1345-9.260734.856514.8491
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resi 1:40
2X-RAY DIFFRACTION2chain A and resi 41:145
3X-RAY DIFFRACTION3chain B and resi 1:40
4X-RAY DIFFRACTION4chain B and resi 41:145

+
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