[English] 日本語
Yorodumi
- PDB-4n09: Structure of Trypanosoma brucei brucei adenosine kinase in comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4n09
TitleStructure of Trypanosoma brucei brucei adenosine kinase in complex with adenosine and AMPPNP
ComponentsAdenosine kinase
KeywordsTRANSFERASE / anion hole / adenosine kinase / adenosine / AMPPNP
Function / homology
Function and homology information


purine ribonucleotide biosynthetic process / adenosine kinase / adenosine kinase activity / glycosome / AMP salvage / ciliary plasm / purine ribonucleoside salvage / purine nucleobase metabolic process / nucleoplasm / ATP binding ...purine ribonucleotide biosynthetic process / adenosine kinase / adenosine kinase activity / glycosome / AMP salvage / ciliary plasm / purine ribonucleoside salvage / purine nucleobase metabolic process / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Adenosine kinase, small domain - #10 / Adenosine kinase / Adenosine kinase, small domain / 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
ADENOSINE / ADENOSINE-5'-DIPHOSPHATE / Adenosine kinase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsTimm, J. / Gonzalez-Pacanowska, D. / Wilson, K.S.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2014
Title: Structures of adenosine kinase from Trypanosoma brucei brucei.
Authors: Timm, J. / Gonzalez-Pacanowska, D. / Wilson, K.S.
History
DepositionOct 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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
B: Adenosine kinase
C: Adenosine kinase
D: Adenosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,81614
Polymers152,9144
Non-polymers2,90210
Water2,666148
1
A: Adenosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9854
Polymers38,2291
Non-polymers7573
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Adenosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9854
Polymers38,2291
Non-polymers7573
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Adenosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9233
Polymers38,2291
Non-polymers6942
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Adenosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9233
Polymers38,2291
Non-polymers6942
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)184.530, 90.220, 98.040
Angle α, β, γ (deg.)90.00, 103.78, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETPROPROAA1 - 3454 - 348
21METMETPROPROBB1 - 3454 - 348
12METMETPROPROAA1 - 3454 - 348
22METMETPROPROCC1 - 3454 - 348
13SERSERPHEPHEAA3 - 3436 - 346
23SERSERPHEPHEDD3 - 3436 - 346
14METMETPROPROBB1 - 3454 - 348
24METMETPROPROCC1 - 3454 - 348
15SERSERPHEPHEBB3 - 3436 - 346
25SERSERPHEPHEDD3 - 3436 - 346
16SERSERPHEPHECC3 - 3436 - 346
26SERSERPHEPHEDD3 - 3436 - 346

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

#1: Protein
Adenosine kinase


Mass: 38228.598 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / Gene: Tb927.6.2360 / Production host: Escherichia coli (E. coli) / References: UniProt: Q584S0, adenosine kinase
#2: Chemical
ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N5O4
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Bis Tris propane, pH 8.5, 0.2 M sodium citrate, 24 % (w/v) polyethylene glycol 3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 13, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.6→65.04 Å / Num. obs: 45507

-
Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
REFMAC5.8.0033refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→65.04 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.926 / SU B: 11.697 / SU ML: 0.238 / Cross valid method: THROUGHOUT / ESU R: 0.922 / ESU R Free: 0.284 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22144 2428 5.1 %RANDOM
Rwork0.1862 ---
obs0.18802 45507 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.964 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å20 Å20.84 Å2
2--0.42 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 2.6→65.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10261 0 192 148 10601
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01910687
X-RAY DIFFRACTIONr_bond_other_d0.0060.029802
X-RAY DIFFRACTIONr_angle_refined_deg1.5311.96714561
X-RAY DIFFRACTIONr_angle_other_deg1.264322397
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.46451377
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.74423.541449
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.814151584
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2661571
X-RAY DIFFRACTIONr_chiral_restr0.0790.21666
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212283
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022492
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9294.3775505
X-RAY DIFFRACTIONr_mcbond_other2.9274.3775504
X-RAY DIFFRACTIONr_mcangle_it4.4856.5666874
X-RAY DIFFRACTIONr_mcangle_other2.1963.4346875
X-RAY DIFFRACTIONr_scbond_it3.7544.6735182
X-RAY DIFFRACTIONr_scbond_other2.0962.4765181
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2453.6347685
X-RAY DIFFRACTIONr_long_range_B_refined4.83918.52811922
X-RAY DIFFRACTIONr_long_range_B_other4.83918.53111923
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A187510.1
12B187510.1
21A188340.1
22C188340.1
31A173720.1
32D173720.1
41B191480.1
42C191480.1
51B177220.11
52D177220.11
61C178180.1
62D178180.1
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 173 -
Rwork0.283 3343 -
obs--99.1 %

+
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