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- PDB-3o15: Crystal Structure of Bacillus subtilis Thiamin Phosphate Synthase... -

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Basic information

Entry
Database: PDB / ID: 3o15
TitleCrystal Structure of Bacillus subtilis Thiamin Phosphate Synthase Complexed with a Carboxylated Thiazole Phosphate
ComponentsThiamine-phosphate pyrophosphorylase
KeywordsTRANSFERASE / thiamin biosynthesis / TIM barrel / protein-intermediate complex
Function / homology
Function and homology information


thiamine phosphate synthase / thiamine-phosphate diphosphorylase activity / thiamine diphosphate biosynthetic process / thiamine biosynthetic process / magnesium ion binding / cytoplasm
Similarity search - Function
Thiamine phosphate synthase / Thiamine phosphate synthase/TenI / Thiamine monophosphate synthase / Thiamin phosphate synthase superfamily / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-3NM / Chem-IFP / PYROPHOSPHATE 2- / Thiamine-phosphate synthase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsMcCulloch, K.M. / Hanes, J.W. / Abdelwahed, S. / Mahanta, N. / Hazra, A. / Ishida, K. / Begley, T.P. / Ealick, S.E.
CitationJournal: to be published
Title: Crystal Structure and Kinetic Characterization of Bacillus subtilis Thiamin Phosphate Synthase with a Carboxylated Thiazole Phosphate
Authors: McCulloch, K.M. / Hanes, J.W. / Abdelwahed, S. / Mahanta, N. / Hazra, A. / Ishida, K. / Begley, T.P. / Ealick, S.E.
History
DepositionJul 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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-phosphate pyrophosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9164
Polymers25,2981
Non-polymers6183
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.020, 96.020, 59.340
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Thiamine-phosphate pyrophosphorylase / TMP pyrophosphorylase / TMP-PPase / Thiamine-phosphate synthase


Mass: 25297.752 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: thiE / Plasmid: pQE-32 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: UniProt: P39594, thiamine phosphate synthase
#2: Chemical ChemComp-3NM / 4-methyl-5-[2-(phosphonooxy)ethyl]-1,3-thiazole-2-carboxylic acid


Mass: 267.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H10NO6PS
#3: Chemical ChemComp-IFP / 2-TRIFLUOROMETHYL-5-METHYLENE-5H-PYRIMIDIN-4-YLIDENEAMINE / 4-IMINO-5-METHIDYL-2-TRIFLUOROMETHYLPYRIMIDINE


Mass: 175.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H4F3N3
#4: Chemical ChemComp-POP / PYROPHOSPHATE 2- / Pyrophosphate


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.7 Å3/Da / Density % sol: 54.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 22-28% PEG4000, 75 mM MgCl2, 1 mM DTT, 100 mM Tris, pH 7.5, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 20400 / % possible obs: 98.3 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.062 / Χ2: 1.168 / Net I/σ(I): 18.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.95-2.023.40.3320061.065199.6
2.02-2.13.40.22820291.2199.8
2.1-2.23.40.17820501.291100
2.2-2.313.50.13620321.4661100
2.31-2.463.50.10920471.4381100
2.46-2.653.40.09520461.431199.7
2.65-2.913.50.07420381.174199.2
2.91-3.333.40.05820611.225198.6
3.33-4.23.40.05320610.785197
4.2-503.40.02820300.577190.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.1data extraction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→28.35 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2317 970 4.7 %
Rwork0.1978 --
obs-19961 96 %
Solvent computationBsol: 56.263 Å2
Displacement parametersBiso max: 75.26 Å2 / Biso mean: 28.8883 Å2 / Biso min: 11.83 Å2
Baniso -1Baniso -2Baniso -3
1-1.506 Å20 Å20 Å2
2--1.506 Å20 Å2
3----3.013 Å2
Refinement stepCycle: LAST / Resolution: 1.95→28.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1635 0 37 212 1884
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.19
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param
X-RAY DIFFRACTION4ligands-try4.param

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