[English] 日本語
Yorodumi
- PDB-8x1g: Human adenylate kinase 1 (hAK1) mutant-R97W -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8x1g
TitleHuman adenylate kinase 1 (hAK1) mutant-R97W
ComponentsAdenylate kinase isoenzyme 1
KeywordsTRANSFERASE / adenylate kinase
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 / cytosol / cytoplasm
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)
MethodSOLUTION NMR / simulated annealing
AuthorsYu, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of human adenylate kinase 1 mutant-R97W.
Authors: Yu, J.
History
DepositionNov 7, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release

-
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
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR relaxation study, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 300structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Adenylate kinase isoenzyme 1


Mass: 21696.891 Da / Num. of mol.: 1 / Mutation: R97W
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
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
123isotropic12D 1H-13C HSQC
132isotropic13D HN(CA)CB
142isotropic13D CBCA(CO)NH
152isotropic13D HNCA
1122isotropic13D HN(CO)CA
1112isotropic13D HNCO
1102isotropic13D HN(CA)CO
192isotropic13D H(CCO)NH
182isotropic13D CC(CO)NH
172isotropic13D HBHA(CO)NH
163isotropic13D (H)CCH-TOCSY
1163isotropic13D CCH-TOCSY
1152isotropic13D 15N-edited NOESY-HSQC
1143isotropic13D 13C-edited NOESY-HSQC
1133isotropic1(HB)CB(CGCD)HD
1173isotropic1(HB)CB(CGCDCE)HE

-
Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.88 mM [U-99% 15N] 15N_R97W, 90% H2O/10% D2O0.88 mM [U-99% 15N] R97W, 10 mM MOPS, 50 mM NaCl, 100 mM Na2SO4, 5 mM EDTA15N_R97W90% H2O/10% D2O
solution20.88 mM [U-99% 13C; U-99% 15N] 15N_13C_R97W10% D2O, 90% H2O/10% D2O0.88 mM [U-99% 13C; U-99% 15N] R97W, 10 mM MOPS, 50 mM NaCl, 100 mM Na2SO4, 5 mM EDTA15N_13C_R97W10% D2O90% H2O/10% D2O
solution30.88 mM [U-99% 13C; U-99% 15N] 15N_13C_R97W99% D2O, 99% D2O0.88 mM [U-99% 13C; U-99% 15N] R97W, 10 mM MOPS, 50 mM NaCl, 100 mM Na2SO4, 5 mM EDTA15N_13C_R97W99% D2O99% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.88 mM15N_R97W[U-99% 15N]1
0.88 mM15N_13C_R97W10% D2O[U-99% 13C; U-99% 15N]2
0.88 mM15N_13C_R97W99% D2O[U-99% 13C; U-99% 15N]3
Sample conditionsIonic strength: 160 mM / Label: MOPS / pH: 6.2 / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 850 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
NMRFAM-SPARKYLee W., Tonelli M., Markley J. L.chemical shift assignment
ARIA2alphaCNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
ARIA2alphaCNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 300 / Conformers submitted total number: 20

+
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