[English] 日本語
Yorodumi
- PDB-5k50: Three-dimensional structure of L-threonine 3-dehydrogenase from T... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5k50
TitleThree-dimensional structure of L-threonine 3-dehydrogenase from Trypanosoma brucei bound to NAD+ and L-allo-threonine refined to 2.23 angstroms
ComponentsL-threonine 3-dehydrogenase
KeywordsOXIDOREDUCTASE / Short-chain dehydrogenase / threonine / holo / ligand-bound
Function / homology
Function and homology information


L-threonine 3-dehydrogenase / L-threonine 3-dehydrogenase activity / L-threonine catabolic process / nucleotide binding
Similarity search - Function
: / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / ALLO-THREONINE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / L-threonine 3-dehydrogenase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsAdjogatse, E.A. / Erskine, P.T. / Cooper, J.B.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Structure and function of L-threonine-3-dehydrogenase from the parasitic protozoan Trypanosoma brucei revealed by X-ray crystallography and geometric simulations.
Authors: Adjogatse, E. / Erskine, P. / Wells, S.A. / Kelly, J.M. / Wilden, J.D. / Chan, A.W.E. / Selwood, D. / Coker, A. / Wood, S. / Cooper, J.B.
History
DepositionMay 22, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 10, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3May 8, 2024Group: 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: L-threonine 3-dehydrogenase
C: L-threonine 3-dehydrogenase
E: L-threonine 3-dehydrogenase
G: L-threonine 3-dehydrogenase
I: L-threonine 3-dehydrogenase
J: L-threonine 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,66026
Polymers213,4686
Non-polymers5,19220
Water7,927440
1
I: L-threonine 3-dehydrogenase
hetero molecules

J: L-threonine 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,9109
Polymers71,1562
Non-polymers1,7547
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,-y,z+11
2
A: L-threonine 3-dehydrogenase
E: L-threonine 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8188
Polymers71,1562
Non-polymers1,6626
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6100 Å2
ΔGint-35 kcal/mol
Surface area24310 Å2
MethodPISA
3
C: L-threonine 3-dehydrogenase
G: L-threonine 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,9319
Polymers71,1562
Non-polymers1,7757
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-30 kcal/mol
Surface area24370 Å2
MethodPISA
4
J: L-threonine 3-dehydrogenase
hetero molecules

I: L-threonine 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,9109
Polymers71,1562
Non-polymers1,7547
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_654-x+1,-y,z-11
Buried area6210 Å2
ΔGint-33 kcal/mol
Surface area24480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.030, 273.060, 55.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

-
Protein , 1 types, 6 molecules ACEGIJ

#1: Protein
L-threonine 3-dehydrogenase


Mass: 35577.965 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: Q7YW97, L-threonine 3-dehydrogenase

-
Non-polymers , 5 types, 460 molecules

#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-ALO / ALLO-THREONINE


Type: L-peptide linking / Mass: 119.119 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H9NO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 440 / 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: 2.23 Å3/Da / Density % sol: 44.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M tri-sodium citrate, 30% w/v PEG 4K, 0.2M ammonium acetate, NAD+ (10mM), L-allo-threonine (30mM)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.26→31.09 Å / Num. obs: 154520 / % possible obs: 90.4 % / Redundancy: 1.9 % / CC1/2: 0.862 / Rmerge(I) obs: 0.151 / Net I/σ(I): 5.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.26-2.341.90.403192.5
12.6-28.820.203191.8

-
Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
Aimless0.1.26data scaling
PDB_EXTRACT3.2data extraction
MOLREPphasing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.26→31.09 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.895 / SU B: 8.565 / SU ML: 0.209 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.357 / ESU R Free: 0.269
RfactorNum. reflection% reflectionSelection details
Rfree0.2808 4815 5 %RANDOM
Rwork0.2073 ---
obs0.211 91289 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 100.74 Å2 / Biso mean: 33.758 Å2 / Biso min: 9.47 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å20 Å2
2--0.03 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 2.26→31.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14958 0 344 440 15742
Biso mean--27.66 30.04 -
Num. residues----1914
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0215692
X-RAY DIFFRACTIONr_bond_other_d0.0020.0214949
X-RAY DIFFRACTIONr_angle_refined_deg1.6492.00821329
X-RAY DIFFRACTIONr_angle_other_deg0.8623.00234390
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.50751916
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.37523.883618
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.765152667
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8961590
X-RAY DIFFRACTIONr_chiral_restr0.0890.22430
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02117197
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023265
X-RAY DIFFRACTIONr_mcbond_it2.1863.2867690
X-RAY DIFFRACTIONr_mcbond_other2.1863.2857685
X-RAY DIFFRACTIONr_mcangle_it3.3874.9179594
LS refinement shellResolution: 2.26→2.318 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 341 -
Rwork0.26 6665 -
all-7006 -
obs--99.86 %

+
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