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- PDB-4hcw: Structure of a eukaryotic thiaminase-I -

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Basic information

Entry
Database: PDB / ID: 4hcw
TitleStructure of a eukaryotic thiaminase-I
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
Biological speciesNaegleria gruberi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS, pseudo-MAD phasing, molecular replacement / Resolution: 2.705 Å
AuthorsKreinbring, C.A. / Hubbard, P.A. / 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 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)235,7116
Polymers235,7116
Non-polymers00
Water00
1
A: thiaminase-I


Theoretical massNumber of molelcules
Total (without water)39,2851
Polymers39,2851
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: thiaminase-I


Theoretical massNumber of molelcules
Total (without water)39,2851
Polymers39,2851
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: thiaminase-I


Theoretical massNumber of molelcules
Total (without water)39,2851
Polymers39,2851
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: thiaminase-I


Theoretical massNumber of molelcules
Total (without water)39,2851
Polymers39,2851
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: thiaminase-I


Theoretical massNumber of molelcules
Total (without water)39,2851
Polymers39,2851
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: thiaminase-I


Theoretical massNumber of molelcules
Total (without water)39,2851
Polymers39,2851
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.56, 203.05, 309.18
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

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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: 3.53 Å3/Da / Density % sol: 65.11 %
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: 23-ID-B / Wavelength: 0.97934 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.7→43.3 Å / Num. obs: 89559 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 14.5 % / Net I/σ(I): 36.5
Reflection shellResolution: 2.7→2.76 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.843 / Mean I/σ(I) obs: 2.4 / % possible all: 97.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
PHENIXAutoSolmodel building
PHENIX(phenix.refine: 1.7.3_928)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXAutoSolphasing
RefinementMethod to determine structure: SIRAS, pseudo-MAD phasing, molecular replacement
Resolution: 2.705→43.3 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2653 4484 5.01 %random
Rwork0.2291 ---
obs0.2309 89479 99.53 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.198 Å2 / ksol: 0.309 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.953 Å20 Å2-0 Å2
2--15.9678 Å20 Å2
3----7.0148 Å2
Refinement stepCycle: LAST / Resolution: 2.705→43.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16344 0 0 0 16344
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00216668
X-RAY DIFFRACTIONf_angle_d0.5722665
X-RAY DIFFRACTIONf_dihedral_angle_d12.0616088
X-RAY DIFFRACTIONf_chiral_restr0.042655
X-RAY DIFFRACTIONf_plane_restr0.0022916
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7052-2.73590.3851400.36662544X-RAY DIFFRACTION90
2.7359-2.76810.3821310.36012795X-RAY DIFFRACTION99
2.7681-2.80180.44171220.35482831X-RAY DIFFRACTION100
2.8018-2.83730.36461530.33562805X-RAY DIFFRACTION100
2.8373-2.87460.39741410.32262794X-RAY DIFFRACTION100
2.8746-2.9140.31061700.30872858X-RAY DIFFRACTION100
2.914-2.95560.34551300.32192788X-RAY DIFFRACTION100
2.9556-2.99970.36411510.31462861X-RAY DIFFRACTION100
2.9997-3.04660.35961520.31742767X-RAY DIFFRACTION100
3.0466-3.09650.38731470.30732844X-RAY DIFFRACTION100
3.0965-3.14990.36391510.30332807X-RAY DIFFRACTION100
3.1499-3.20720.30711600.30152817X-RAY DIFFRACTION100
3.2072-3.26880.35591480.29482878X-RAY DIFFRACTION100
3.2688-3.33550.34191600.28012799X-RAY DIFFRACTION100
3.3355-3.4080.31031590.28922783X-RAY DIFFRACTION100
3.408-3.48730.30231450.26942855X-RAY DIFFRACTION100
3.4873-3.57440.31291570.27342831X-RAY DIFFRACTION100
3.5744-3.6710.31871470.26542821X-RAY DIFFRACTION100
3.671-3.7790.26821440.24392850X-RAY DIFFRACTION100
3.779-3.90090.26981580.21552833X-RAY DIFFRACTION100
3.9009-4.04020.26371460.21472846X-RAY DIFFRACTION100
4.0402-4.20190.26031480.20712845X-RAY DIFFRACTION100
4.2019-4.39290.21011530.20022864X-RAY DIFFRACTION100
4.3929-4.62430.22381470.17712837X-RAY DIFFRACTION100
4.6243-4.91360.21091630.17872850X-RAY DIFFRACTION100
4.9136-5.29240.20621680.1862840X-RAY DIFFRACTION100
5.2924-5.82390.23411650.19722894X-RAY DIFFRACTION100
5.8239-6.6640.2821420.21652901X-RAY DIFFRACTION100
6.664-8.38590.19491380.17582926X-RAY DIFFRACTION100
8.3859-43.3110.21021480.19553031X-RAY DIFFRACTION99

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