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- PDB-2g9z: Thiamin pyrophosphokinase from Candida albicans -

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Basic information

Entry
Database: PDB / ID: 2g9z
TitleThiamin pyrophosphokinase from Candida albicans
Componentsthiamine pyrophosphokinase
KeywordsTRANSFERASE / Thiamin-PNP / TPK / Thiamin pyrophosphokinase / structural genomics / PROFUN / 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
PHOSPHATE ION / Chem-VNP / :
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 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
DepositionMar 7, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 4, 2006Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.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.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_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: thiamine pyrophosphokinase
B: thiamine pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,87214
Polymers79,6162
Non-polymers1,25512
Water9,368520
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7180 Å2
ΔGint-114 kcal/mol
Surface area23690 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)50.825, 60.331, 63.722
Angle α, β, γ (deg.)66.14, 89.94, 65.07
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein thiamine pyrophosphokinase


Mass: 39808.234 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

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Non-polymers , 5 types, 532 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-VNP / 3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-(2-{[HYDROXY(PHOSPHONOAMINO)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3-THIAZOL-3-I UM / THIAMIN-PNP / [2-[3-[(4-AMINO-2-METHYL-PYRIMIDIN-5-YL)METHYL]-4-METHYL-1-THIA-3-AZON IACYCLOPENTA-2,4-DIEN-5-YL]ETHOXY-HYDROXY-PHOSPHORYL]AMINOPHOSPHONIC ACID


Mass: 424.330 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H20N5O6P2S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 520 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsIDENTICAL TO THE SEQUENCE FROM CANDIDA ALBICANS SC5314

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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: 1.99 Å3/Da / Density % sol: 38.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 17.5% PEG4000, 0.2M Magnesium chloride, 0.1M Tris, 10% Glycerol, Protein incubated with Thiamin and AMP-PNP, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.95372 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 5, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.96→29.44 Å / Num. all: 40488 / Num. obs: 40488 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.035 / Rsym value: 0.035 / Net I/σ(I): 14.5
Reflection shellResolution: 1.96→2.03 Å / Redundancy: 1 % / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 3.8 / Num. unique all: 52 / Rsym value: 0.195 / % possible all: 60.3

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMAC5refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IG0

1ig0


Resolution: 1.96→29.44 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: maximum likelihood target using amplitudes
RfactorNum. reflection% reflectionSelection details
Rfree0.236 4073 -random
Rwork0.187 ---
all0.236 44107 --
obs0.187 40488 91.8 %-
Displacement parametersBiso mean: 28.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.28 Å2-3.48 Å21.2 Å2
2--0.07 Å2-0.2 Å2
3---2.23 Å2
Refinement stepCycle: LAST / Resolution: 1.96→29.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4775 0 70 520 5365
LS refinement shellResolution: 1.96→2.03 Å / Rfactor Rfree error: 0.004
RfactorNum. reflection% reflection
Rfree0.236 4073 -
Rwork0.187 --
obs-40488 91.7 %

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