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- PDB-3nm3: The Crystal Structure of Candida glabrata THI6, a Bifunctional En... -

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Basic information

Entry
Database: PDB / ID: 3nm3
TitleThe Crystal Structure of Candida glabrata THI6, a Bifunctional Enzyme involved in Thiamin Biosyhthesis of Eukaryotes
ComponentsThiamine biosynthetic bifunctional enzyme
KeywordsTRANSFERASE / THI6 / Bifunctional Enzyme / Thiamin Biosynthesis / Eukaryoyes
Function / homology
Function and homology information


hydroxyethylthiazole kinase activity / thiamine-phosphate diphosphorylase activity / thiamine diphosphate biosynthetic process / thiamine biosynthetic process / magnesium ion binding / ATP binding / cytosol
Similarity search - Function
Thiamine phosphate synthase / Hydroxyethylthiazole kinase / Hydroxyethylthiazole kinase family / Thiamine phosphate synthase/TenI / Thiamine monophosphate synthase / Thiamin phosphate synthase superfamily / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / Aldolase class I ...Thiamine phosphate synthase / Hydroxyethylthiazole kinase / Hydroxyethylthiazole kinase family / Thiamine phosphate synthase/TenI / Thiamine monophosphate synthase / Thiamin phosphate synthase superfamily / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYROPHOSPHATE 2- / THIAMIN PHOSPHATE / Candida glabrata strain CBS138 chromosome E complete sequence
Similarity search - Component
Biological speciesCandida glabrata (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.102 Å
AuthorsPaul, D. / Chatterjee, A. / Begley, T.P. / Ealick, S.E.
CitationJournal: Biochemistry / Year: 2010
Title: Domain Organization in Candida glabrata THI6, a Bifunctional Enzyme Required for Thiamin Biosynthesis in Eukaryotes .
Authors: Paul, D. / Chatterjee, A. / Begley, T.P. / Ealick, S.E.
History
DepositionJun 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 29, 2013Group: Other
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Thiamine biosynthetic bifunctional enzyme
B: Thiamine biosynthetic bifunctional enzyme
C: Thiamine biosynthetic bifunctional enzyme
D: Thiamine biosynthetic bifunctional enzyme
E: Thiamine biosynthetic bifunctional enzyme
F: Thiamine biosynthetic bifunctional enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)352,03324
Polymers348,7606
Non-polymers3,27418
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20730 Å2
ΔGint-120 kcal/mol
Surface area107640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.191, 154.602, 148.650
Angle α, β, γ (deg.)90.00, 102.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Thiamine biosynthetic bifunctional enzyme


Mass: 58126.605 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida glabrata (fungus) / Gene: CAGL0E05808g, THI6 / Plasmid: THT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Star(DE3)
References: UniProt: Q6FV03, thiamine phosphate synthase, hydroxyethylthiazole kinase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-TPS / THIAMIN PHOSPHATE


Mass: 345.334 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C12H18N4O4PS
#4: Chemical
ChemComp-POP / PYROPHOSPHATE 2- / Pyrophosphate


Mass: 175.959 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: H2O7P2

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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: 63.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% PEG400, 200 mM MgCl2, 100 mM HEPES, pH 7.5, vapor diffusion, hanging drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 12, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.1→46 Å / Num. all: 188896 / Num. obs: 72303 / Biso Wilson estimate: 69.15 Å2

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 3.102→46 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7892 / SU ML: 2.95 / σ(F): 0.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2513 3404 5.02 %
Rwork0.1974 --
obs0.2001 67768 80.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.183 Å2 / ksol: 0.299 e/Å3
Displacement parametersBiso max: 156.09 Å2 / Biso mean: 84.8153 Å2 / Biso min: 48.56 Å2
Baniso -1Baniso -2Baniso -3
1-34.4952 Å2-0 Å223.8834 Å2
2---11.1247 Å20 Å2
3----23.3705 Å2
Refinement stepCycle: LAST / Resolution: 3.102→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22799 0 192 0 22991
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00723518
X-RAY DIFFRACTIONf_angle_d1.11531960
X-RAY DIFFRACTIONf_chiral_restr0.0693798
X-RAY DIFFRACTIONf_plane_restr0.0054098
X-RAY DIFFRACTIONf_dihedral_angle_d19.3278482
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1024-3.14670.4187830.3831646172950
3.1467-3.19360.4094970.34062004210160
3.1936-3.24350.3691960.3122082217863
3.2435-3.29670.36651210.29652193231465
3.2967-3.35350.34011150.27982287240269
3.3535-3.41450.28361250.26572272239769
3.4145-3.48010.29341330.26852340247371
3.4801-3.55110.2871320.23352359249171
3.5511-3.62830.32981230.24212424254773
3.6283-3.71270.27571310.22922543267477
3.7127-3.80550.30881290.21562637276679
3.8055-3.90830.26691540.20742676283081
3.9083-4.02330.24711480.20112813296185
4.0233-4.1530.23811700.18262889305988
4.153-4.30140.25191510.162998314990
4.3014-4.47350.22781360.14623105324192
4.4735-4.67690.18821890.13933081327093
4.6769-4.92320.18951650.1443077324293
4.9232-5.23120.22071570.15323146330394
5.2312-5.63450.23011660.16123171333795
5.6345-6.20030.23911910.16993144333595
6.2003-7.09470.23041700.16213192336295
7.0947-8.92790.15861690.13833206337596
8.9279-46.07930.21871530.17013079323290

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