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- PDB-3hpd: Structure of hydroxyethylthiazole kinase protein from pyrococcus ... -

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Basic information

Entry
Database: PDB / ID: 3hpd
TitleStructure of hydroxyethylthiazole kinase protein from pyrococcus horikoshii OT3
ComponentsHydroxyethylthiazole kinase
KeywordsTRANSFERASE / ALPHA-BETA / ATP BINDING / KINASE / ATP-binding / Magnesium / Metal-binding / Nucleotide-binding / Thiamine biosynthesis / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


hydroxyethylthiazole kinase / hydroxyethylthiazole kinase activity / thiamine biosynthetic process / thiamine diphosphate biosynthetic process / magnesium ion binding / ATP binding
Similarity search - Function
Hydroxyethylthiazole kinase / Hydroxyethylthiazole kinase family / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Hydroxyethylthiazole kinase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsJeyakanthan, J. / Thamotharan, S. / Kuramitsu, S. / Yokoyama, S. / Tahirov, T.H. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Structure of Hydroxyethylthiazole Kinase Protein from Pyrococcus Horikoshii Ot3
Authors: Jeyakanthan, J. / Kuramitsu, S. / Yokoyama, S.
History
DepositionJun 4, 2009Deposition site: RCSB / Processing site: PDBJ
SupersessionJun 16, 2009ID: 1V8A
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Hydroxyethylthiazole kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0852
Polymers28,9901
Non-polymers951
Water3,747208
1
A: Hydroxyethylthiazole kinase
hetero molecules

A: Hydroxyethylthiazole kinase
hetero molecules

A: Hydroxyethylthiazole kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,2566
Polymers86,9713
Non-polymers2853
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation11_566y,-z+1,-x+11
Buried area6860 Å2
ΔGint-49 kcal/mol
Surface area25910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.242, 112.242, 112.242
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-302-

HOH

21A-392-

HOH

31A-395-

HOH

41A-412-

HOH

51A-434-

HOH

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Components

#1: Protein Hydroxyethylthiazole kinase / 4-methyl-5-beta-hydroxyethylthiazole kinase / Thz kinase / TH kinase


Mass: 28990.275 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: PET-11A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODON PLUS(DE3)-RIL / References: UniProt: O58877, hydroxyethylthiazole kinase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.03 Å3/Da / Density % sol: 39.48 %
Crystal growTemperature: 295 K / Method: microbatch method / pH: 9.3
Details: 0.88M SODIUMCITRATE, 0.1M CHESS, pH 9.3, MICROBATCH METHOD, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Nov 27, 2003 / Details: Mirrors
RadiationMonochromator: Si (1 1 1), GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→19.84 Å / Num. obs: 20162 / % possible obs: 99.8 % / Biso Wilson estimate: 11.3 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.067
Reflection shellResolution: 1.85→1.92 Å / Rmerge(I) obs: 0.324 / Num. unique all: 2004 / Rsym value: 0.292 / % possible all: 99.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1C3Q

1c3q


Resolution: 1.85→19.84 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 853468.49 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.184 963 4.9 %RANDOM
Rwork0.164 ---
obs0.164 19747 97.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.8931 Å2 / ksol: 0.402666 e/Å3
Displacement parametersBiso mean: 19.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.85→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1946 0 5 208 2159
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_mcbond_it1.131.5
X-RAY DIFFRACTIONc_mcangle_it1.662
X-RAY DIFFRACTIONc_scbond_it2.252
X-RAY DIFFRACTIONc_scangle_it3.432.5
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.212 165 5.3 %
Rwork0.181 2943 -
obs--93.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3po4.parampo4.top

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