[English] 日本語
Yorodumi
- PDB-4wql: Crystal structure of aminoglycoside nucleotidylyltransferase ANT(... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4wql
TitleCrystal structure of aminoglycoside nucleotidylyltransferase ANT(2")-Ia, kanamycin-bound
Components2''-aminoglycoside nucleotidyltransferase
Keywordstransferase/transferase inhibitor / antibiotic resistance / aminoglycosides / kanamycin / nucleotidylyltransferase / adenylyltransferase / nucleotidyltransferase fold / alpha/beta protein / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID / National Institute of Allergy and Infectious Diseases / NIAID / transferase-transferase inhibitor complex
Function / homology
Function and homology information


gentamicin 2''-nucleotidyltransferase / aminoglycoside 2''-nucleotidyltransferase activity / response to antibiotic / metal ion binding
Similarity search - Function
Aminoglycoside-2''-adenylyltransferase / Aminoglycoside-2''-adenylyltransferase / Beta Polymerase; domain 2 - #40 / Beta Polymerase; domain 2 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / KANAMYCIN A / 2''-aminoglycoside nucleotidyltransferase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsCox, G. / Stogios, P.J. / Savchenko, A. / Wright, G.D. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support Canada, 2items
OrganizationGrant numberCountry
Canada Foundation for Innovation26332 Canada
Canadian Institutes of Health Research (CIHR)MT-13536 Canada
CitationJournal: Mbio / Year: 2015
Title: Structural and Molecular Basis for Resistance to Aminoglycoside Antibiotics by the Adenylyltransferase ANT(2)-Ia.
Authors: Cox, G. / Stogios, P.J. / Savchenko, A. / Wright, G.D.
History
DepositionOct 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Other
Revision 1.2Jan 28, 2015Group: Database references
Revision 1.3Feb 22, 2017Group: Structure summary
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 27, 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_struct_conn_angle / refine_hist / 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_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 2''-aminoglycoside nucleotidyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,21214
Polymers19,9501
Non-polymers1,26213
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-0 kcal/mol
Surface area9440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.460, 42.010, 47.810
Angle α, β, γ (deg.)90.00, 105.25, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein 2''-aminoglycoside nucleotidyltransferase / AAD(2'') / Gentamicin 2''-nucleotidyltransferase / Gentamicin resistance protein


Mass: 19950.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: aadB / Plasmid: pDEST15 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): Rosetta
References: UniProt: P0AE05, gentamicin 2''-nucleotidyltransferase

-
Non-polymers , 5 types, 249 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-KAN / KANAMYCIN A


Mass: 484.499 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H36N4O11 / Comment: antibiotic*YM
#4: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 60 mg/mL protein, 10% 2-propanol, 20% PEG 4K, 0.1 M HEPES pH 7.5, 15 mM kanamycin B (5:1 molar ratio kanamycin B:protein)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.548 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.548 Å / Relative weight: 1
ReflectionResolution: 1.73→25 Å / Num. obs: 35472 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 2.3 % / Biso Wilson estimate: 19.44 Å2 / Rsym value: 0.064 / Net I/σ(I): 33.4
Reflection shellResolution: 1.73→1.76 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 3.57 / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
Cootmodel building
PHENIX(phenix.refine: 1.9_1692)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: apoprotein

Resolution: 1.73→23.463 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.184 1784 5.04 %Random selection
Rwork0.1477 ---
obs0.1495 35415 99.37 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.17 Å2
Refinement stepCycle: LAST / Resolution: 1.73→23.463 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1385 0 83 236 1704
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.021512
X-RAY DIFFRACTIONf_angle_d1.6682055
X-RAY DIFFRACTIONf_dihedral_angle_d13.553555
X-RAY DIFFRACTIONf_chiral_restr0.101223
X-RAY DIFFRACTIONf_plane_restr0.008258
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.77680.33071390.2842553X-RAY DIFFRACTION97
1.7768-1.8290.28181470.242556X-RAY DIFFRACTION99
1.829-1.8880.2641270.20342574X-RAY DIFFRACTION99
1.888-1.95550.21741400.17492546X-RAY DIFFRACTION99
1.9555-2.03370.20541420.17712574X-RAY DIFFRACTION99
2.0337-2.12620.19071300.15252638X-RAY DIFFRACTION100
2.1262-2.23830.22381410.14312569X-RAY DIFFRACTION100
2.2383-2.37840.17331320.14282637X-RAY DIFFRACTION100
2.3784-2.56180.25771220.14272602X-RAY DIFFRACTION100
2.5618-2.81920.1571390.13812629X-RAY DIFFRACTION100
2.8192-3.22630.13561380.13172574X-RAY DIFFRACTION100
3.2263-4.06130.17571410.11322595X-RAY DIFFRACTION100
4.0613-23.4650.14081460.14362584X-RAY DIFFRACTION100
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)
12.2890.9401-0.54514.3008-0.52722.55490.0330.02130.122-0.0673-0.01040.1597-0.0637-0.0773-0.03430.07530.0063-0.00140.1068-0.01170.09168.35593.026916.6624
26.5487-2.261-2.85244.39755.25977.04330.04430.2451-0.2057-0.2908-0.31080.6448-0.2041-0.57590.35390.18040.0032-0.01040.2187-0.01750.2459-3.3963-1.567613.7772
30.2891-0.0394-0.0791.8720.38091.72250.01040.00140.0048-0.0444-0.03640.02340.07890.01850.02820.10740.00520.01110.12420.00350.129214.7806-3.059310.1776
45.3018-0.38141.55494.22225.58888.33810.23960.2325-0.3151-0.4976-0.19690.52240.028-0.73190.00770.26410.0013-0.04860.22070.02210.22829.07835.9294-6.2374
54.8362.0343-0.64282.9151.84212.6859-0.09590.1702-0.1507-0.58190.1367-0.3405-0.18990.1202-0.04870.1640.02040.01220.15920.02490.087821.0112-1.8428-4.3733
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 3:61)
2X-RAY DIFFRACTION2(chain A and resid 62:82)
3X-RAY DIFFRACTION3(chain A and resid 83:136)
4X-RAY DIFFRACTION4(chain A and resid 137:152)
5X-RAY DIFFRACTION5(chain A and resid 153:177)

+
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