[English] 日本語
Yorodumi
- PDB-4hcy: Structure of a eukaryotic thiaminase-I bound to the thiamin analo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4hcy
TitleStructure of a eukaryotic thiaminase-I bound to the thiamin analogue 3-deazathiamin
Componentsthiaminase-I
KeywordsTRANSFERASE / thiamine pyridinylase
Function / homology
Function and homology information


transketolase / transketolase activity / pentose-phosphate shunt / metal ion binding / cytosol
Similarity search - Function
D-Maltodextrin-Binding Protein; domain 2 - #220 / : / Thiaminase I-like, N-terminal domain / Transketolase, bacterial-like / Transketolase family / : / Transketolase-like TK C-terminal domain / : / Transketolase signature 1. / Transketolase, N-terminal ...D-Maltodextrin-Binding Protein; domain 2 - #220 / : / Thiaminase I-like, N-terminal domain / Transketolase, bacterial-like / Transketolase family / : / Transketolase-like TK C-terminal domain / : / Transketolase signature 1. / Transketolase, N-terminal / Transketolase, thiamine diphosphate binding domain / Transketolase binding site / Transketolase signature 2. / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain / Transketolase, pyrimidine binding domain / Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II / Thiamin diphosphate-binding fold / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-0YN / transketolase
Similarity search - Component
Biological speciesNaegleria gruberi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.75 Å
AuthorsKreinbring, C.A. / Hubbard, P.A. / Leeper, F.J. / Hawksley, D. / Petsko, G.A. / Ringe, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structure of a eukaryotic thiaminase I.
Authors: Kreinbring, C.A. / Remillard, S.P. / Hubbard, P. / Brodkin, H.R. / Leeper, F.J. / Hawksley, D. / Lai, E.Y. / Fulton, C. / Petsko, G.A. / Ringe, D.
History
DepositionOct 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Feb 5, 2014Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: thiaminase-I
B: thiaminase-I
C: thiaminase-I
D: thiaminase-I
E: thiaminase-I
F: thiaminase-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,29112
Polymers235,7116
Non-polymers1,5806
Water00
1
A: thiaminase-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5482
Polymers39,2851
Non-polymers2631
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: thiaminase-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5482
Polymers39,2851
Non-polymers2631
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: thiaminase-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5482
Polymers39,2851
Non-polymers2631
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: thiaminase-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5482
Polymers39,2851
Non-polymers2631
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: thiaminase-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5482
Polymers39,2851
Non-polymers2631
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: thiaminase-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5482
Polymers39,2851
Non-polymers2631
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.09, 201.86, 305.24
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein
thiaminase-I


Mass: 39285.109 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Naegleria gruberi (eukaryote) / Gene: NAEGRDRAFT_78612 / Plasmid: pET19b / Production host: Escherichia coli (E. coli) / Strain (production host): BLR(DE3)(recA-) / References: UniProt: D2V4Z5, thiamine pyridinylase
#2: Chemical
ChemComp-0YN / 2-{4-[(4-amino-2-methylpyrimidin-5-yl)methyl]-3-methylthiophen-2-yl}ethanol


Mass: 263.359 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C13H17N3OS

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.39 Å3/Da / Density % sol: 63.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.7 M ammonium sulfate, 15% (v/v) glycerol, 1.7% (v/v) PEG 400, 85 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 18, 2004 / Details: Bent conical Si-mirror (Rh coated)
RadiationMonochromator: Bent Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.75→42.09 Å / Num. obs: 82491 / % possible obs: 98.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.4 % / Rmerge(I) obs: 0.098
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 11.2 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 7898 / % possible all: 95.3

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.3_928)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 4HCW

4hcw


Resolution: 2.75→42.09 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2673 4123 5 %random
Rwork0.2316 ---
obs0.2334 82402 98.46 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.369 Å2 / ksol: 0.3 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--10.0919 Å20 Å2-0 Å2
2--17.4221 Å20 Å2
3----7.3303 Å2
Refinement stepCycle: LAST / Resolution: 2.75→42.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16339 0 108 0 16447
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00216758
X-RAY DIFFRACTIONf_angle_d0.66922788
X-RAY DIFFRACTIONf_dihedral_angle_d12.0466096
X-RAY DIFFRACTIONf_chiral_restr0.0412653
X-RAY DIFFRACTIONf_plane_restr0.0032924
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7497-2.78210.39041480.36562532X-RAY DIFFRACTION94
2.7821-2.8160.38561520.34882575X-RAY DIFFRACTION94
2.816-2.85160.38311190.34582597X-RAY DIFFRACTION96
2.8516-2.88910.40611030.32942619X-RAY DIFFRACTION95
2.8891-2.92870.38451330.32522631X-RAY DIFFRACTION96
2.9287-2.97050.3851210.31932629X-RAY DIFFRACTION96
2.9705-3.01490.36771300.32212620X-RAY DIFFRACTION97
3.0149-3.0620.34811580.31122654X-RAY DIFFRACTION97
3.062-3.11210.351570.30242613X-RAY DIFFRACTION98
3.1121-3.16580.35781460.29862693X-RAY DIFFRACTION98
3.1658-3.22330.34311420.29142665X-RAY DIFFRACTION99
3.2233-3.28530.30891450.28832683X-RAY DIFFRACTION99
3.2853-3.35230.33221510.28252693X-RAY DIFFRACTION99
3.3523-3.42520.36141380.27842698X-RAY DIFFRACTION99
3.4252-3.50480.34731400.28252720X-RAY DIFFRACTION100
3.5048-3.59240.32761330.26342733X-RAY DIFFRACTION100
3.5924-3.68950.271330.24692716X-RAY DIFFRACTION100
3.6895-3.7980.2691550.23512738X-RAY DIFFRACTION100
3.798-3.92050.25121500.21252723X-RAY DIFFRACTION100
3.9205-4.06050.25831520.20972737X-RAY DIFFRACTION100
4.0605-4.2230.19291440.20242735X-RAY DIFFRACTION100
4.223-4.4150.24141370.19022749X-RAY DIFFRACTION100
4.415-4.64750.20781360.17452756X-RAY DIFFRACTION100
4.6475-4.93820.20861560.1882748X-RAY DIFFRACTION100
4.9382-5.31880.26091480.20232758X-RAY DIFFRACTION100
5.3188-5.85280.2521370.21472784X-RAY DIFFRACTION100
5.8528-6.69680.25451400.21552807X-RAY DIFFRACTION100
6.6968-8.42610.21581580.18152793X-RAY DIFFRACTION100
8.4261-42.09770.20291610.19042880X-RAY DIFFRACTION98

+
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