[English] 日本語
Yorodumi
- PDB-5lpa: AadA E87Q in complex with ATP, calcium and dihydrostreptomycin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5lpa
TitleAadA E87Q in complex with ATP, calcium and dihydrostreptomycin
ComponentsStreptomycin 3''-adenylyltransferase
KeywordsTRANSFERASE / AMINOGLYCOSIDE ADENYL TRANSFERASE / ANT(3'')9 / ANTIBIOTIC RESISTANCE
Function / homology
Function and homology information


streptomycin 3''-adenylyltransferase / aminoglycoside 3''-adenylyltransferase activity / adenylyltransferase activity / response to antibiotic / ATP binding / metal ion binding
Similarity search - Function
Adenylyltransferase AadA/Aad9 / Adenylyltransferase AadA, C-terminal domain / Aminoglycoside adenylyltransferase, C-terminal domain / Polymerase, nucleotidyl transferase domain / Nucleotidyltransferase domain / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
dihydrostreptomycin / ADENOSINE-5'-TRIPHOSPHATE / Aminoglycoside (3'') (9) adenylyltransferase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsStern, A.L. / Van der Verren, S.E. / Selmer, M.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council Sweden
Knut and Alice Wallenberg FoundationRiboCORE Sweden
Citation
Journal: J.Biol.Chem. / Year: 2018
Title: Structural mechanism of AadA, a dual-specificity aminoglycoside adenylyltransferase fromSalmonella enterica.
Authors: Stern, A.L. / Van der Verren, S.E. / Kanchugal P, S. / Nasvall, J. / Gutierrez-de-Teran, H. / Selmer, M.
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2015
Title: Structure of AadA from Salmonella enterica: a monomeric aminoglycoside (3'')(9) adenyltransferase.
Authors: Chen, Y. / Nasvall, J. / Wu, S. / Andersson, D.I. / Selmer, M.
History
DepositionAug 12, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.2Jan 10, 2024Group: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_conn.ptnr2_label_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Streptomycin 3''-adenylyltransferase
B: Streptomycin 3''-adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,82915
Polymers61,2302
Non-polymers2,59913
Water12,556697
1
A: Streptomycin 3''-adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8847
Polymers30,6151
Non-polymers1,2686
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Streptomycin 3''-adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9468
Polymers30,6151
Non-polymers1,3317
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.885, 82.885, 79.782
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Streptomycin 3''-adenylyltransferase


Mass: 30615.158 Da / Num. of mol.: 2 / Mutation: E87Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: aadA, STM1264 / Plasmid: PEXP5-CT / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8ZPX9, streptomycin 3''-adenylyltransferase

-
Non-polymers , 6 types, 710 molecules

#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-71R / dihydrostreptomycin


Mass: 583.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H41N7O12
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 697 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.4 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop
Details: 20% (w/v) PEG 6000, 0.2 M Calcium chloride, 0.1 M Hepes pH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.4→41.442 Å / Num. obs: 120821 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.19 % / Biso Wilson estimate: 12.86 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Net I/σ(I): 11.4
Reflection shellResolution: 1.4→1.5 Å / Redundancy: 5.18 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.14 / CC1/2: 0.727 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5g4a

5g4a


Resolution: 1.4→41.442 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 17.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1782 5960 4.94 %Random selection
Rwork0.146 ---
obs0.1476 120743 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→41.442 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4231 0 160 697 5088
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144804
X-RAY DIFFRACTIONf_angle_d1.3816616
X-RAY DIFFRACTIONf_dihedral_angle_d15.7631850
X-RAY DIFFRACTIONf_chiral_restr0.099756
X-RAY DIFFRACTIONf_plane_restr0.008872
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.41590.26732000.22313839X-RAY DIFFRACTION100
1.4159-1.43260.2481820.21943846X-RAY DIFFRACTION100
1.4326-1.450.23962080.20223874X-RAY DIFFRACTION100
1.45-1.46840.25272060.1893745X-RAY DIFFRACTION100
1.4684-1.48770.25641940.18183819X-RAY DIFFRACTION100
1.4877-1.50810.20531600.17283929X-RAY DIFFRACTION100
1.5081-1.52970.22782260.16363735X-RAY DIFFRACTION100
1.5297-1.55250.23752200.16153806X-RAY DIFFRACTION100
1.5525-1.57670.20341880.15783914X-RAY DIFFRACTION100
1.5767-1.60260.19412020.14333766X-RAY DIFFRACTION100
1.6026-1.63020.18561760.13023860X-RAY DIFFRACTION100
1.6302-1.65990.17361790.12533832X-RAY DIFFRACTION100
1.6599-1.69180.16842160.12023849X-RAY DIFFRACTION100
1.6918-1.72630.15811840.11283816X-RAY DIFFRACTION100
1.7263-1.76390.1612300.1193799X-RAY DIFFRACTION100
1.7639-1.80490.18281720.12013849X-RAY DIFFRACTION100
1.8049-1.850.15072100.12133813X-RAY DIFFRACTION100
1.85-1.90010.16751940.13483821X-RAY DIFFRACTION100
1.9001-1.9560.19282120.13593815X-RAY DIFFRACTION100
1.956-2.01910.17361740.12653886X-RAY DIFFRACTION100
2.0191-2.09130.15262160.12513791X-RAY DIFFRACTION100
2.0913-2.1750.18821860.13823837X-RAY DIFFRACTION100
2.175-2.2740.17141470.13263852X-RAY DIFFRACTION100
2.274-2.39390.18062160.13963826X-RAY DIFFRACTION100
2.3939-2.54380.17491840.14513799X-RAY DIFFRACTION100
2.5438-2.74020.17772010.15013881X-RAY DIFFRACTION100
2.7402-3.01590.17512100.16063782X-RAY DIFFRACTION100
3.0159-3.45210.18152230.15593802X-RAY DIFFRACTION100
3.4521-4.34850.15312200.14493816X-RAY DIFFRACTION100
4.3485-41.46060.16982240.15593784X-RAY DIFFRACTION100

+
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