[English] 日本語
Yorodumi
- PDB-7de3: Human adenylate kinase 1 (hAK1) mutant-R128W -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7de3
TitleHuman adenylate kinase 1 (hAK1) mutant-R128W
ComponentsAdenylate kinase isoenzyme 1
KeywordsTRANSFERASE / cellular energy homeostasis / adenine nucleotide metabolism / CELL CYCLE
Function / homology
Function and homology information


nucleoside-phosphate kinase / dAMP kinase activity / outer dense fiber / AMP metabolic process / ADP biosynthetic process / nucleoside triphosphate biosynthetic process / adenylate kinase / AMP kinase activity / nucleobase-containing small molecule interconversion / nucleoside-diphosphate kinase ...nucleoside-phosphate kinase / dAMP kinase activity / outer dense fiber / AMP metabolic process / ADP biosynthetic process / nucleoside triphosphate biosynthetic process / adenylate kinase / AMP kinase activity / nucleobase-containing small molecule interconversion / nucleoside-diphosphate kinase / Interconversion of nucleotide di- and triphosphates / nucleoside diphosphate kinase activity / ATP metabolic process / extracellular exosome / ATP binding / cytoplasm / cytosol
Similarity search - Function
Adenylate kinase isoenzyme 1 / Adenylate kinase, isozyme 1/5 / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP kinase / Adenylate kinase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Adenylate kinase isoenzyme 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.197 Å
AuthorsLin, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of human adenylate kinase 1 mutant-R128W.
Authors: Lin, W.
History
DepositionNov 1, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Adenylate kinase isoenzyme 1


Theoretical massNumber of molelcules
Total (without water)21,6971
Polymers21,6971
Non-polymers00
Water3,063170
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10390 Å2
Unit cell
Length a, b, c (Å)95.167, 95.167, 47.961
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-339-

HOH

21A-350-

HOH

-
Components

#1: Protein Adenylate kinase isoenzyme 1 / AK 1 / ATP-AMP transphosphorylase 1 / ATP:AMP phosphotransferase / Adenylate monophosphate kinase / Myokinase


Mass: 21696.891 Da / Num. of mol.: 1 / Mutation: R128W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AK1 / Production host: Escherichia coli (E. coli)
References: UniProt: P00568, adenylate kinase, nucleoside-diphosphate kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.5 Å3/Da / Density % sol: 50.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG 3350,0.2M Ammonium acetate / PH range: 6.6-8.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Jun 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.197→33.647 Å / Num. obs: 11451 / % possible obs: 97.69 % / Redundancy: 13.5 % / CC1/2: 0.938 / Net I/σ(I): 17
Reflection shellResolution: 2.197→2.275 Å / Rmerge(I) obs: 0.154 / Num. unique obs: 22139

-
Processing

Software
NameVersionClassification
PHENIX1.16-3549refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3adk

3adk


Resolution: 2.197→33.647 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2595 --
Rwork0.205 --
obs-11451 97.69 %
Displacement parametersBiso max: 89.08 Å2 / Biso mean: 32.0887 Å2 / Biso min: 9.39 Å2
Refinement stepCycle: LAST / Resolution: 2.197→33.647 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1455 0 0 170 1625

+
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