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- PDB-4hcy: Structure of a eukaryotic thiaminase-I bound to the thiamin analo... -

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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 / metal ion binding
Similarity search - Function
D-Maltodextrin-Binding Protein; domain 2 - #220 / Transketolase, bacterial-like / Transketolase family / Transketolase signature 1. / Transketolase, thiamine diphosphate binding domain / Transketolase binding site / Transketolase signature 2. / Transketolase, N-terminal / Transketolase, C-terminal domain / Transketolase, C-terminal domain ...D-Maltodextrin-Binding Protein; domain 2 - #220 / Transketolase, bacterial-like / Transketolase family / Transketolase signature 1. / Transketolase, thiamine diphosphate binding domain / Transketolase binding site / Transketolase signature 2. / Transketolase, N-terminal / Transketolase, C-terminal domain / Transketolase, C-terminal domain / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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