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- PDB-2hh9: Thiamin pyrophosphokinase from Candida albicans -

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Basic information

Entry
Database: PDB / ID: 2hh9
TitleThiamin pyrophosphokinase from Candida albicans
ComponentsThiamin pyrophosphokinaseThiamine diphosphokinase
KeywordsTRANSFERASE / Thiamin / TPK / Thiamin pyrophosphokinase / Structural Genomics / Bacterial targets at IGS-CNRS / France / BIGS
Function / homology
Function and homology information


Thiamin pyrophosphokinase, thiamin-binding domain / Thiamin pyrophosphokinase, catalytic domain / Jelly Rolls / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAbergel, C. / Santini, S. / Monchois, V. / Rousselle, T. / Claverie, J.M. / Bacterial targets at IGS-CNRS, France (BIGS)
CitationJournal: Bmc Struct.Biol. / Year: 2008
Title: Structural characterization of CA1462, the Candida albicans thiamine pyrophosphokinase.
Authors: Santini, S. / Monchois, V. / Mouz, N. / Sigoillot, C. / Rousselle, T. / Claverie, J.M. / Abergel, C.
History
DepositionJun 28, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_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_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_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: Thiamin pyrophosphokinase
B: Thiamin pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,4198
Polymers77,7912
Non-polymers6286
Water11,890660
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5620 Å2
ΔGint-53 kcal/mol
Surface area24610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.309, 60.696, 64.831
Angle α, β, γ (deg.)65.94, 89.86, 64.87
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Thiamin pyrophosphokinase / Thiamine diphosphokinase / Hypothetical protein THI80


Mass: 38895.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Strain: NIH3147 / Gene: CA1462 / Plasmid: pSF04, PQE80 / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K12 / References: UniProt: Q59N99, thiamine diphosphokinase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-VIB / 3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM / THIAMIN / VITAMIN B1 / Thiamine


Mass: 265.355 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H17N4OS / Comment: medication*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 660 / Source method: isolated from a natural source / Formula: H2O

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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: 2.16 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG4000, 0.2M Magnesium chloride, 0.1M Tris, 20% Glycerol. Protein incubated with Thiman, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.95372 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 27, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.1→57.74 Å / Num. all: 70311 / Num. obs: 35489 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 18.5
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 2 % / Rmerge(I) obs: 0.083 / Mean I/σ(I) obs: 8.9 / Num. unique all: 4617 / Rsym value: 0.083 / % possible all: 85.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G9Z

2g9z


Resolution: 2.1→50.19 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1184662.66 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 3541 10 %RANDOM
Rwork0.183 ---
obs0.183 35488 96 %-
all-36939 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 73.7166 Å2 / ksol: 0.35623 e/Å3
Displacement parametersBiso mean: 28.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å2-0.58 Å20 Å2
2---0.68 Å20.14 Å2
3---0.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2.1→50.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4786 0 40 660 5486
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.252 508 9.5 %
Rwork0.2 4851 -
obs--86.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4VIB.paramVIB.top

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