[English] 日本語
Yorodumi
- PDB-3uq9: Adenosine kinase from Schistosoma mansoni in complex with tubercidin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3uq9
TitleAdenosine kinase from Schistosoma mansoni in complex with tubercidin
ComponentsAdenosine kinase, putative
KeywordsTRANSFERASE / ribokinase
Function / homology
Function and homology information


adenosine kinase / adenosine kinase activity / purine ribonucleoside salvage / nucleotide binding
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
Chem-TBN / : / Adenosine kinase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.343 Å
AuthorsRomanello, L. / Cassago, A. / Bachega, F.R. / Garatt, R.C. / DeMarco, R. / Pereira, H.M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Adenosine kinase from Schistosoma mansoni: structural basis for the differential incorporation of nucleoside analogues.
Authors: Romanello, L. / Bachega, J.F. / Cassago, A. / Brandao-Neto, J. / Demarco, R. / Garratt, R.C. / Pereira, H.D.
History
DepositionNov 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references
Revision 1.2Jan 16, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Adenosine kinase, putative
B: Adenosine kinase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,0897
Polymers83,2192
Non-polymers8705
Water5,837324
1
A: Adenosine kinase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1784
Polymers41,6101
Non-polymers5683
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Adenosine kinase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9113
Polymers41,6101
Non-polymers3022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.556, 180.509, 78.552
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Adenosine kinase, putative /


Mass: 41609.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: 37oC / Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: Adenosine kinase, Smp_008360 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: C4PZB4, UniProt: G4V7G8*PLUS, adenosine kinase
#2: Chemical ChemComp-TBN / '2-(4-AMINO-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3,4-DIOL / 7-DEAZAADENOSINE


Mass: 266.253 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H14N4O4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 2.54 Å3/Da / Density % sol: 51.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100mM Bis-tris pH 6.1-6.7, 200mM LiSO4, 16-20% PEG 3350 , VAPOR DIFFUSION, SITTING DROP, temperature 293K
PH range: 6.1-6.7

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 11, 2011 / Details: mirrors
RadiationMonochromator: VariMax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.34→20 Å / Num. all: 36510 / Num. obs: 35262 / % possible obs: 96.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3 / Biso Wilson estimate: 37.35 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 11.82
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.34-2.480.3522.38188.2
2.48-2.650.2523.6197.5
2.65-2.860.1935.11199.5
2.86-3.130.147.33199.7
3.13-3.480.08312.41199.6
3.48-40.0519.36198.7
4-4.850.03426.21198.3
4.85-6.660.03525.74197.5
6.660.02433.47188

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
XSCALEdata scaling
PHASERphasing
DMphasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.343→19.638 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.28 / σ(F): 1.99 / Phase error: 20.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2265 1764 5.01 %
Rwork0.1713 --
obs0.1741 35239 96.79 %
all-36510 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.7556 Å2
Baniso -1Baniso -2Baniso -3
1-7.6486 Å2-0 Å2-0 Å2
2---2.9689 Å2-0 Å2
3----4.6515 Å2
Refinement stepCycle: LAST / Resolution: 2.343→19.638 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5305 0 59 324 5688
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045472
X-RAY DIFFRACTIONf_angle_d0.7847405
X-RAY DIFFRACTIONf_dihedral_angle_d11.4571948
X-RAY DIFFRACTIONf_chiral_restr0.056836
X-RAY DIFFRACTIONf_plane_restr0.003934
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3428-2.40610.3121130.22652145X-RAY DIFFRACTION82
2.4061-2.47670.27271300.21732462X-RAY DIFFRACTION94
2.4767-2.55650.24691320.20432513X-RAY DIFFRACTION96
2.5565-2.64770.2661350.19992563X-RAY DIFFRACTION98
2.6477-2.75340.26161390.18972621X-RAY DIFFRACTION99
2.7534-2.87840.25251370.19632611X-RAY DIFFRACTION100
2.8784-3.02960.23641400.19682654X-RAY DIFFRACTION100
3.0296-3.21860.25831370.18852606X-RAY DIFFRACTION100
3.2186-3.46590.2211400.16712649X-RAY DIFFRACTION100
3.4659-3.81240.2291390.15622646X-RAY DIFFRACTION99
3.8124-4.35880.1751390.14392641X-RAY DIFFRACTION98
4.3588-5.47190.19351410.13372676X-RAY DIFFRACTION98
5.4719-19.63870.20611420.16852688X-RAY DIFFRACTION95

+
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