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- PDB-3rm5: Structure of Trifunctional THI20 from Yeast -

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Basic information

Entry
Database: PDB / ID: 3rm5
TitleStructure of Trifunctional THI20 from Yeast
ComponentsHydroxymethylpyrimidine/phosphomethylpyrimidine kinase THI20
KeywordsTRANSFERASE / HMP Kinase (ThiD) / Thiaminase II
Function / homology
Function and homology information


thiamine catabolic process / phosphooxymethylpyrimidine kinase / hydroxymethylpyrimidine kinase / phosphomethylpyrimidine kinase activity / aminopyrimidine aminohydrolase / thiaminase activity / hydroxymethylpyrimidine kinase activity / thiamine biosynthetic process / thiamine diphosphate biosynthetic process / ATP binding / cytosol
Similarity search - Function
Hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase domain / Thiaminase II / Thiaminase-2/PQQC / TENA/THI-4/PQQC family / Pyridoxamine kinase/Phosphomethylpyrimidine kinase / Phosphomethylpyrimidine kinase / Heme oxygenase-like / Heme Oxygenase; Chain A / Haem oxygenase-like, multi-helical / Ribokinase ...Hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase domain / Thiaminase II / Thiaminase-2/PQQC / TENA/THI-4/PQQC family / Pyridoxamine kinase/Phosphomethylpyrimidine kinase / Phosphomethylpyrimidine kinase / Heme oxygenase-like / Heme Oxygenase; Chain A / Haem oxygenase-like, multi-helical / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase THI20
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.68 Å
AuthorsFrench, J.B. / Begley, T.P. / Ealick, S.E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Structure of trifunctional THI20 from yeast.
Authors: French, J.B. / Begley, T.P. / Ealick, S.E.
History
DepositionApr 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Other
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 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: Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase THI20
B: Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase THI20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,7085
Polymers122,4202
Non-polymers2883
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14220 Å2
ΔGint-137 kcal/mol
Surface area40700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.704, 140.096, 143.273
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase THI20 / Hydroxymethylpyrimidine kinase / HMP kinase / Hydroxymethylpyrimidine phosphate kinase / HMP-P ...Hydroxymethylpyrimidine kinase / HMP kinase / Hydroxymethylpyrimidine phosphate kinase / HMP-P kinase / HMP-phosphate kinase / HMPP kinase


Mass: 61209.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: O1239, THI20, Thi20p, YOL055C / Production host: Escherichia coli (E. coli)
References: UniProt: Q08224, hydroxymethylpyrimidine kinase, phosphooxymethylpyrimidine kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.45 Å3/Da / Density % sol: 49.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10-14% Peg 8K, 0.2 M Calcium Acetate, 0.1 M Imidazole, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 20, 2009
RadiationMonochromator: CRYO-COOLED SI(111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionRedundancy: 2.8 % / Av σ(I) over netI: 12.15 / Number: 87487 / Rmerge(I) obs: 0.094 / Χ2: 1.24 / D res high: 2.7 Å / D res low: 50 Å / Num. obs: 31670 / % possible obs: 92.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.81509210.0561.5863.1
4.625.8195.910.0781.5343.2
4.034.6296.710.0831.6343.2
3.664.0397.710.1071.4813.2
3.43.6698.310.1491.183.2
3.23.498.810.2020.893.1
3.043.297.810.2250.7832.6
2.913.0494.510.2570.7162.2
2.82.9186.210.2810.5971.9
2.72.87010.3290.9551.5
ReflectionResolution: 2.68→100.17 Å / Num. obs: 31670 / % possible obs: 92.8 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.094 / Χ2: 1.237 / Net I/σ(I): 7.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.68-2.81.50.32923480.955170
2.8-2.911.90.28128770.597186.2
2.91-3.042.20.25731860.716194.5
3.04-3.22.60.22532710.783197.8
3.2-3.43.10.20233410.89198.8
3.4-3.663.20.14933301.18198.3
3.66-4.033.20.10733411.481197.7
4.03-4.623.20.08332931.634196.7
4.62-5.813.20.07833241.534195.9
5.81-503.10.05633591.586192

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.5.0110refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1YAF, 1JXH

1yaf

1jxh


Resolution: 2.68→50 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.887 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 31.284 / SU ML: 0.296 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.401 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2786 1606 5.1 %RANDOM
Rwork0.2377 ---
obs0.2398 31625 91.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 110.87 Å2 / Biso mean: 55.3917 Å2 / Biso min: 27.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å20 Å2
2---1.36 Å20 Å2
3---1.61 Å2
Refinement stepCycle: LAST / Resolution: 2.68→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7794 0 15 57 7866
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0227974
X-RAY DIFFRACTIONr_angle_refined_deg0.9121.96310867
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3651031
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.73624.595309
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.051151225
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.811525
X-RAY DIFFRACTIONr_chiral_restr0.0590.21259
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215992
X-RAY DIFFRACTIONr_mcbond_it0.2381.55172
X-RAY DIFFRACTIONr_mcangle_it0.44128261
X-RAY DIFFRACTIONr_scbond_it0.42232802
X-RAY DIFFRACTIONr_scangle_it0.7414.52606
LS refinement shellResolution: 2.68→2.749 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 75 -
Rwork0.295 1230 -
all-1305 -
obs--52.18 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.34530.16120.16771.55260.11990.120.00370.0148-0.0612-0.22390.01970.0297-0.05790.0562-0.02330.1353-0.03820.01270.10470.03770.0432-28.324415.756216.7037
20.3401-0.10540.07191.10810.44790.25590.0059-0.0739-0.09950.13840.0194-0.0630.0110.001-0.02530.0994-0.0004-0.04480.11960.07150.0772-20.28277.766439.5666
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 551
2X-RAY DIFFRACTION2B2 - 551

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