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- PDB-2yxz: Crystal structure of tt0281 from Thermus thermophilus HB8 -

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Basic information

Entry
Database: PDB / ID: 2yxz
TitleCrystal structure of tt0281 from Thermus thermophilus HB8
ComponentsThiamin-monophosphate kinase
KeywordsTRANSFERASE / alpha/beta structure
Function / homology
Function and homology information


thiamine-phosphate kinase / thiamine-phosphate kinase activity / thiamine diphosphate biosynthetic process / thiamine biosynthetic process / magnesium ion binding / ATP binding
Similarity search - Function
Thiamine-monophosphate kinase / Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2 / PurM-like C-terminal domain / PurM-like, N-terminal domain / PurM-like, N-terminal domain / AIR synthase related protein, N-terminal domain / PurM-like, C-terminal domain / PurM-like, C-terminal domain superfamily / PurM-like, N-terminal domain superfamily / AIR synthase related protein, C-terminal domain ...Thiamine-monophosphate kinase / Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2 / PurM-like C-terminal domain / PurM-like, N-terminal domain / PurM-like, N-terminal domain / AIR synthase related protein, N-terminal domain / PurM-like, C-terminal domain / PurM-like, C-terminal domain superfamily / PurM-like, N-terminal domain superfamily / AIR synthase related protein, C-terminal domain / 60s Ribosomal Protein L30; Chain: A; / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Thiamine-monophosphate kinase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.9 Å
AuthorsGoto, M.
CitationJournal: to be published
Title: Crystal structure of tt0281 from Thermus thermophilus HB8
Authors: Matsushita, T. / Kan, M. / Goto, M. / Miyahara, I. / Kamiya, N.
History
DepositionApr 27, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thiamin-monophosphate kinase
B: Thiamin-monophosphate kinase
C: Thiamin-monophosphate kinase
D: Thiamin-monophosphate kinase


Theoretical massNumber of molelcules
Total (without water)131,8644
Polymers131,8644
Non-polymers00
Water7,530418
1
A: Thiamin-monophosphate kinase
C: Thiamin-monophosphate kinase


Theoretical massNumber of molelcules
Total (without water)65,9322
Polymers65,9322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-38.1 kcal/mol
Surface area22890 Å2
MethodPISA
2
B: Thiamin-monophosphate kinase
D: Thiamin-monophosphate kinase


Theoretical massNumber of molelcules
Total (without water)65,9322
Polymers65,9322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-41.6 kcal/mol
Surface area22500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.564, 52.190, 181.124
Angle α, β, γ (deg.)90.00, 108.33, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Thiamin-monophosphate kinase


Mass: 32965.895 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gamiTM(DE3) / References: UniProt: Q5SL69, thiamine-phosphate kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / 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: 2.41 Å3/Da / Density % sol: 48.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Ammonium Sulfate, Dioxane, HEPES-Na, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 4, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→171.499 Å / Num. all: 99656 / Num. obs: 91864 / % possible obs: 92.2 % / Biso Wilson estimate: 18.7 Å2
Reflection shellResolution: 1.9→1.97 Å / % possible all: 76.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: MIR / Resolution: 1.9→48.65 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2328165.93 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.264 9188 10 %RANDOM
Rwork0.225 ---
obs0.225 91864 92.4 %-
all-99656 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.5457 Å2 / ksol: 0.380872 e/Å3
Displacement parametersBiso mean: 35.7 Å2
Baniso -1Baniso -2Baniso -3
1-10.4 Å20 Å2-7.79 Å2
2---0.37 Å20 Å2
3----10.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 1.9→48.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8836 0 0 418 9254
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_d23.2
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it1.211.5
X-RAY DIFFRACTIONc_mcangle_it1.782
X-RAY DIFFRACTIONc_scbond_it1.862
X-RAY DIFFRACTIONc_scangle_it2.722.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.335 1322 10.1 %
Rwork0.299 11782 -
obs--79.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwat.top
X-RAY DIFFRACTION3ion.paramion.top

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