[English] 日本語
Yorodumi
- PDB-1j7i: Crystal Structure of 3',5"-Aminoglycoside Phosphotransferase Type... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1j7i
TitleCrystal Structure of 3',5"-Aminoglycoside Phosphotransferase Type IIIa Apoenzyme
ComponentsAMINOGLYCOSIDE 3'-PHOSPHOTRANSFERASE
KeywordsTRANSFERASE / antibiotic resistance / kinase / ATP-binding
Function / homology
Function and homology information


kanamycin kinase / kanamycin kinase activity / response to antibiotic / ATP binding
Similarity search - Function
Aminoglycoside 3-phosphotransferase / : / Aminoglycoside phosphotransferase / Phosphotransferase enzyme family / Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 / Aminoglycoside phosphotransferase (APH), C-terminal lobe / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase-like domain superfamily / Alpha-Beta Complex ...Aminoglycoside 3-phosphotransferase / : / Aminoglycoside phosphotransferase / Phosphotransferase enzyme family / Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 / Aminoglycoside phosphotransferase (APH), C-terminal lobe / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase-like domain superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Aminoglycoside 3'-phosphotransferase
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsBurk, D.L. / Hon, W.C. / Leung, A.K.-W. / Berghuis, A.M.
Citation
Journal: Biochemistry / Year: 2001
Title: Structural analyses of nucleotide binding to an aminoglycoside phosphotransferase.
Authors: Burk, D.L. / Hon, W.C. / Leung, A.K. / Berghuis, A.M.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1997
Title: Structure of an Enzyme Required for Antibiotic Resistance Reveals Homology to Eukaryotic Protein Kinases
Authors: Hon, W.C. / McKay, G.A. / Thompson, P.R. / Sweet, R.M. / Yang, D.S. / Wright, G.D. / Berghuis, A.M.
History
DepositionMay 16, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AMINOGLYCOSIDE 3'-PHOSPHOTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)31,0121
Polymers31,0121
Non-polymers00
Water00
1
A: AMINOGLYCOSIDE 3'-PHOSPHOTRANSFERASE

A: AMINOGLYCOSIDE 3'-PHOSPHOTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)62,0242
Polymers62,0242
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_645y+1,x-1,-z1
Unit cell
Length a, b, c (Å)55.662, 55.662, 185.228
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein AMINOGLYCOSIDE 3'-PHOSPHOTRANSFERASE / APH(3')III


Mass: 31012.045 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Plasmid: pPCRG6 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A3Y5, kanamycin kinase

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: HEPES, magnesium chloride, ammonium sulfate, isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
18 mg/mlprotein1drop
25 mMHEPES1drop
310 mM1dropMgCl2
42 Mammonium sulfate1reservoir(w/v)
55 %(v/v)2-propanol1reservoir

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 5165 / Num. obs: 5165 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 7.2
Reflection shellResolution: 3.2→3.31 Å / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 2.3 / % possible all: 96.7
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 15937
Reflection shell
*PLUS
Highest resolution: 3.2 Å / % possible obs: 96.7 %

-
Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→35.6 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 73178.08 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.306 503 10.4 %RANDOM
Rwork0.219 ---
all-4829 --
obs-4829 91.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 128.9 Å2 / ksol: 0.3476 e/Å3
Displacement parametersBiso mean: 30.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å20 Å20 Å2
2--0.83 Å20 Å2
3----1.66 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 3.2→35.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2148 0 0 0 2148
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d1.24
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.337 67 9.7 %
Rwork0.271 622 -
obs--81.7 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10.4 % / Rfactor obs: 0.219
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 30.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.341
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.24
LS refinement shell
*PLUS
Rfactor Rfree: 0.337 / % reflection Rfree: 9.7 % / Rfactor Rwork: 0.271

+
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