[English] 日本語
Yorodumi
- PDB-5kb6: High-resolution structure of the adenosine kinase from Mus muscul... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5kb6
TitleHigh-resolution structure of the adenosine kinase from Mus musculus in complex with adenosine
ComponentsAdenosine kinase
KeywordsTRANSFERASE / Adenosine Kinase
Function / homology
Function and homology information


dATP biosynthetic process / Purine salvage / Ribavirin ADME / adenosine kinase / adenosine kinase activity / dAMP salvage / deoxyadenosine kinase activity / adenosine metabolic process / GMP salvage / type B pancreatic cell proliferation ...dATP biosynthetic process / Purine salvage / Ribavirin ADME / adenosine kinase / adenosine kinase activity / dAMP salvage / deoxyadenosine kinase activity / adenosine metabolic process / GMP salvage / type B pancreatic cell proliferation / AMP salvage / purine ribonucleoside salvage / positive regulation of cardiac muscle hypertrophy / purine nucleobase metabolic process / positive regulation of T cell proliferation / phosphorylation / nucleoplasm / ATP binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Adenosine kinase / Adenosine kinase, small domain - #10 / Adenosine kinase, small domain / pfkB family of carbohydrate kinases signature 2. / Carbohydrate/purine kinase, PfkB, conserved site / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase ...Adenosine kinase / Adenosine kinase, small domain - #10 / Adenosine kinase, small domain / pfkB family of carbohydrate kinases signature 2. / Carbohydrate/purine kinase, PfkB, conserved site / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / ADENOSINE / Adenosine kinase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.2 Å
AuthorsOliveira, R.R. / Neto, R.M. / Polo, C.C. / Tonoli, C.C.C. / Murakami, M.T. / Franchini, K.G.
CitationJournal: To Be Published
Title: High-resolution structure of the adenosine kinase from Mus musculus in complex with adenosine
Authors: Oliveira, R.R. / Neto, R.M. / Polo, C.C. / Tonoli, C.C.C. / Murakami, M.T. / Franchini, K.G.
History
DepositionJun 2, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: 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: Adenosine kinase
B: Adenosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,18813
Polymers80,6902
Non-polymers1,49811
Water8,665481
1
A: Adenosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1917
Polymers40,3451
Non-polymers8466
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Adenosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9976
Polymers40,3451
Non-polymers6525
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.839, 82.159, 89.189
Angle α, β, γ (deg.)90.000, 92.690, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Adenosine kinase / / AK / Adenosine 5'-phosphotransferase


Mass: 40344.777 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Adk / Production host: Escherichia coli (E. coli) / References: UniProt: P55264, adenosine kinase

-
Non-polymers , 6 types, 492 molecules

#2: Chemical ChemComp-ADN / ADENOSINE / Adenosine


Mass: 267.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O4
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 481 / 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: 2.44 Å3/Da / Density % sol: 49.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 50% (v/v) PEG400 0.2 M lithium sulphate 0.1 M sodium acetate 2.5 mM adenosine

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 0.954 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 228026 / % possible obs: 99.8 % / Redundancy: 4 % / Rmerge(I) obs: 0.054 / Net I/av σ(I): 22.889 / Net I/σ(I): 12
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.2-1.223.80.653199.9
1.22-1.243.90.5811100
1.24-1.2740.5371100
1.27-1.293.90.495199.9
1.29-1.323.90.4331100
1.32-1.353.90.3851100
1.35-1.393.90.3431100
1.39-1.423.90.2971100
1.42-1.463.90.2551100
1.46-1.513.90.2111100
1.51-1.573.90.1771100
1.57-1.633.80.1521100
1.63-1.73.80.1281100
1.7-1.793.90.1091100
1.79-1.940.0841100
1.9-2.054.20.0621100
2.05-2.264.40.0521100
2.26-2.594.50.0461100
2.59-3.264.50.041100
3.26-504.30.032197.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
MOLREPphasing
DENZOdata reduction
RefinementResolution: 1.2→20.76 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.416 / SU ML: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.033 / ESU R Free: 0.032
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1589 11429 5 %RANDOM
Rwork0.1408 ---
obs0.1417 216557 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 94.68 Å2 / Biso mean: 19.828 Å2 / Biso min: 8.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å2-0 Å2-0.13 Å2
2---0.1 Å20 Å2
3----0.1 Å2
Refinement stepCycle: final / Resolution: 1.2→20.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5390 0 176 481 6047
Biso mean--21.82 31.54 -
Num. residues----686
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195669
X-RAY DIFFRACTIONr_bond_other_d0.0020.025413
X-RAY DIFFRACTIONr_angle_refined_deg1.3871.9657676
X-RAY DIFFRACTIONr_angle_other_deg0.918312469
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6715707
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.58324.779272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.57715964
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6571529
X-RAY DIFFRACTIONr_chiral_restr0.0870.2851
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026458
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021317
X-RAY DIFFRACTIONr_mcbond_it1.0991.6462771
X-RAY DIFFRACTIONr_mcbond_other1.0951.6442768
X-RAY DIFFRACTIONr_mcangle_it1.5142.4763465
X-RAY DIFFRACTIONr_rigid_bond_restr1.963311082
X-RAY DIFFRACTIONr_sphericity_free29.465143
X-RAY DIFFRACTIONr_sphericity_bonded11.226511303
LS refinement shellResolution: 1.199→1.23 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 809 -
Rwork0.274 15719 -
all-16528 -
obs--98.4 %

+
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