[English] 日本語
Yorodumi
- PDB-8gil: L-threonine 3-Dehydrogenase from Trypanosoma cruzi (apo form) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8gil
TitleL-threonine 3-Dehydrogenase from Trypanosoma cruzi (apo form)
ComponentsL-threonine 3-dehydrogenase
KeywordsOXIDOREDUCTASE / threonine / dehydrogenase / trypanossoma / apo
Function / homologyNAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding domain superfamily / : / L-threonine 3-dehydrogenase, putative
Function and homology information
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsFaria, J.N. / Mercaldi, G.F. / Fagundes, M. / Bezerra, E.H.S. / Cordeiro, A.T.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2018/22202-8 Brazil
Sao Paulo Research Foundation (FAPESP)2021/14741-9 Brazil
CitationJournal: To Be Published
Title: Structure, allosteric regulation and metabolic activity of L-threonine 3-Dehydrogenase from Trypanosoma cruzi
Authors: Faria, J.N. / Mercaldi, G.F. / Fagundes, M. / Eufrasio, A.G. / Cordeiro, A.T.
History
DepositionMar 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: L-threonine 3-dehydrogenase
B: L-threonine 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,0854
Polymers81,0072
Non-polymers782
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-14 kcal/mol
Surface area25170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.685, 81.834, 83.674
Angle α, β, γ (deg.)90.000, 90.546, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein L-threonine 3-dehydrogenase /


Mass: 40503.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: Tc00.1047053507923.10 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4CU39, L-threonine 3-dehydrogenase
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.976 Å3/Da / Density % sol: 37.781 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG 3350, 200 mM ammonium acetate and 100 mM Bis-Tris pH 5.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS SIRIUS / Beamline: MANACA / Wavelength: 0.97718 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97718 Å / Relative weight: 1
ReflectionResolution: 2.1→46.73 Å / Num. obs: 36424 / % possible obs: 99.1 % / Redundancy: 4.7 % / CC1/2: 0.995 / Net I/σ(I): 8.4
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 4.5 % / Num. unique obs: 2927 / CC1/2: 0.595 / % possible all: 98.6

-
Processing

Software
NameVersionClassification
MxCuBEdata collection
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMAC5.8.0258refinement
Cootmodel building
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→46.727 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.917 / Cross valid method: THROUGHOUT / ESU R: 0.257 / ESU R Free: 0.213
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2581 2004 5.51 %
Rwork0.1998 34365 -
all0.203 --
obs-36369 98.719 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 31.969 Å2
Baniso -1Baniso -2Baniso -3
1--0.286 Å20 Å21.531 Å2
2--1.449 Å2-0 Å2
3----1.191 Å2
Refinement stepCycle: LAST / Resolution: 2.1→46.727 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4977 0 2 86 5065
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0135093
X-RAY DIFFRACTIONr_bond_other_d0.0350.0174779
X-RAY DIFFRACTIONr_angle_refined_deg1.7441.6516903
X-RAY DIFFRACTIONr_angle_other_deg2.3641.57811099
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1925636
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.5521.44250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.34415875
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4161536
X-RAY DIFFRACTIONr_chiral_restr0.1440.2660
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025670
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021054
X-RAY DIFFRACTIONr_nbd_refined0.2330.21141
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2350.24581
X-RAY DIFFRACTIONr_nbtor_refined0.1870.22513
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.22360
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2195
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.050.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2270.218
X-RAY DIFFRACTIONr_nbd_other0.250.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.110.25
X-RAY DIFFRACTIONr_mcbond_it2.3843.3532550
X-RAY DIFFRACTIONr_mcbond_other2.3833.3512549
X-RAY DIFFRACTIONr_mcangle_it3.5275.0193184
X-RAY DIFFRACTIONr_mcangle_other3.5265.0213185
X-RAY DIFFRACTIONr_scbond_it3.1413.522543
X-RAY DIFFRACTIONr_scbond_other3.1413.522543
X-RAY DIFFRACTIONr_scangle_it4.5675.1683719
X-RAY DIFFRACTIONr_scangle_other4.5655.1683719
X-RAY DIFFRACTIONr_lrange_it6.57739.2465786
X-RAY DIFFRACTIONr_lrange_other6.55939.2355773
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.1540.3121440.292508X-RAY DIFFRACTION98.368
2.154-2.2130.3431870.2942436X-RAY DIFFRACTION98.461
2.213-2.2780.4921110.4282320X-RAY DIFFRACTION96.5449
2.278-2.3480.2851530.2552349X-RAY DIFFRACTION98.9324
2.348-2.4250.2671760.2232215X-RAY DIFFRACTION99.0062
2.425-2.510.2721290.2072164X-RAY DIFFRACTION99.0069
2.51-2.6040.2511100.2042158X-RAY DIFFRACTION98.9961
2.604-2.710.2581310.192028X-RAY DIFFRACTION99.2188
2.71-2.8310.2871010.1861964X-RAY DIFFRACTION99.1835
2.831-2.9690.2731250.2051851X-RAY DIFFRACTION99.2466
2.969-3.1290.264840.1961827X-RAY DIFFRACTION99.2212
3.129-3.3190.276840.191704X-RAY DIFFRACTION99.0582
3.319-3.5480.212750.1781593X-RAY DIFFRACTION98.8152
3.548-3.8310.272800.1791454X-RAY DIFFRACTION98.0192
3.831-4.1960.217670.1631384X-RAY DIFFRACTION99.0444
4.196-4.690.173600.1441265X-RAY DIFFRACTION99.3253
4.69-5.4120.191540.1581085X-RAY DIFFRACTION99.476
5.412-6.6220.26590.192934X-RAY DIFFRACTION99.2008
6.622-9.3360.195470.155722X-RAY DIFFRACTION98.9704
9.336-46.7270.247270.175405X-RAY DIFFRACTION97.7376

+
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