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- PDB-1ub0: Crystal Structure Analysis of Phosphomethylpyrimidine Kinase (Thi... -

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Basic information

Entry
Database: PDB / ID: 1ub0
TitleCrystal Structure Analysis of Phosphomethylpyrimidine Kinase (ThiD) from Thermus Thermophilus Hb8
ComponentsPhosphomethylpyrimidine Kinase
KeywordsTRANSFERASE / Thiamin biosynthesis / ThiD / Ribokinase family / Phosphorylation / structural genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


phosphomethylpyrimidine kinase activity / thiamine biosynthetic process
Similarity search - Function
Hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase domain / Pyridoxamine kinase/Phosphomethylpyrimidine kinase / Phosphomethylpyrimidine kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / Transferase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsBagautdinov, B. / Kuramitsu, S. / Yokoyama, S. / Miyano, M. / Tahirov, T.H. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure Analysis of Phosphomethylpyrimidine Kinase (ThiD) from Thermus Thermophilus Hb8
Authors: Bagautdinov, B. / Kuramitsu, S. / Yokoyama, S. / Miyano, M. / Tahirov, T.H.
History
DepositionMar 26, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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
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: Phosphomethylpyrimidine Kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4578
Polymers26,8161
Non-polymers6417
Water1,982110
1
A: Phosphomethylpyrimidine Kinase
hetero molecules

A: Phosphomethylpyrimidine Kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,91316
Polymers53,6322
Non-polymers1,28114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_675x-y+1,-y+2,-z1
Buried area6990 Å2
ΔGint-54 kcal/mol
Surface area18300 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)105.145, 105.145, 105.469
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsThe biological assembly is a dimer generated from the molecule in the asymmetric unit

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Components

#1: Protein Phosphomethylpyrimidine Kinase / ThiD


Mass: 26816.041 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: ThiD / Plasmid: PET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: Q7SIA0, phosphooxymethylpyrimidine kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 3.07 Å3/Da / Density % sol: 59.64 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 5.3
Details: Ammonium sulfate 1.58M, citrate 0.1M, dioxane 10v/v (%), pH 5.3, MICROBATCH, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 12, 2002 / Details: mirrors
RadiationMonochromator: fixed exit double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→40 Å / Num. all: 476469 / Num. obs: 476454 / % possible obs: 99.99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 21.52 % / Biso Wilson estimate: 31.2 Å2 / Rmerge(I) obs: 0.055
Reflection shellResolution: 2.05→2.14 Å / Redundancy: 3.03 % / Rmerge(I) obs: 0.482 / Num. unique all: 2174 / % possible all: 91.9

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Processing

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

1jxi


Resolution: 2.05→40 Å / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The electron density is poor for sidechain atoms of residues: LYS A117, LEU A139, ARG A189
RfactorNum. reflection% reflectionSelection details
Rfree0.2316 1046 -RANDOM
Rwork0.2066 ---
all-22162 --
obs-21300 96.1 %-
Displacement parametersBiso mean: 43.3 Å2
Baniso -1Baniso -2Baniso -3
1-3.74 Å22.42 Å20 Å2
2--3.74 Å20 Å2
3----7.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.05→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1805 0 41 110 1956
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d1.2
X-RAY DIFFRACTIONc_angle_deg0.005
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_improper_angle_d0.82
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
2.05-2.140.2661160.2350.025249191.9
2.14-2.260.2811230.2390.025253093.4
2.26-2.40.231170.2250.021255593.4
2.4-2.580.2541390.2170.022260695.7
2.58-2.840.2351430.20.02266997.3
2.84-3.250.2591110.20.025271298.4

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