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- PDB-8ogh: Truncated 1-deoxy-D-xylulose 5-phosphate synthase (DXPS) from Myc... -

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Basic information

Entry
Database: PDB / ID: 8ogh
TitleTruncated 1-deoxy-D-xylulose 5-phosphate synthase (DXPS) from Mycobacterium tuberculosis with butylacetylphosphonate (BAP) bound
Components1-deoxy-D-xylulose-5-phosphate synthase
KeywordsTRANSFERASE / complex / inhibitor / thdp / mep-pathway
Function / homology
Function and homology information


1-deoxy-D-xylulose-5-phosphate synthase / 1-deoxy-D-xylulose-5-phosphate synthase activity / 1-deoxy-D-xylulose 5-phosphate biosynthetic process / thiamine binding / chlorophyll biosynthetic process / thiamine biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / thiamine pyrophosphate binding / manganese ion binding ...1-deoxy-D-xylulose-5-phosphate synthase / 1-deoxy-D-xylulose-5-phosphate synthase activity / 1-deoxy-D-xylulose 5-phosphate biosynthetic process / thiamine binding / chlorophyll biosynthetic process / thiamine biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / thiamine pyrophosphate binding / manganese ion binding / positive regulation of gene expression / magnesium ion binding / cytosol
Similarity search - Function
Deoxyxylulose-5-phosphate synthase / 1-deoxy-D-xylulose-5-phosphate synthase / : / Transketolase signature 1. / Transketolase binding site / Transketolase signature 2. / Transketolase, C-terminal domain / Transketolase, C-terminal domain / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain ...Deoxyxylulose-5-phosphate synthase / 1-deoxy-D-xylulose-5-phosphate synthase / : / Transketolase signature 1. / Transketolase binding site / Transketolase signature 2. / Transketolase, C-terminal domain / Transketolase, C-terminal domain / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain / Transketolase, pyrimidine binding domain / Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II / Thiamin diphosphate-binding fold
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Chem-VMI / 1-deoxy-D-xylulose-5-phosphate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsGawriljuk, O.V. / Oerlemans, R. / Groves, R.M.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission860816European Union
CitationJournal: Crystals / Year: 2023
Title: Structure of Mycobacterium tuberculosis 1-Deoxy-D-Xylulose 5-Phosphate Synthase in Complex with Butylacetylphosphonate
Authors: Gawriljuk, V.O. / Oerlemans, R. / Gierse, R.M. / Jotwani, R. / Hirsch, A.K.H. / Groves, M.R.
History
DepositionMar 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 2.0Oct 25, 2023Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_entity_nonpoly
Item: _chem_comp.formula / _chem_comp.name ..._chem_comp.formula / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 1-deoxy-D-xylulose-5-phosphate synthase
B: 1-deoxy-D-xylulose-5-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,44918
Polymers127,3702
Non-polymers2,07816
Water23,7441318
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11090 Å2
ΔGint-37 kcal/mol
Surface area35400 Å2
Unit cell
Length a, b, c (Å)63.462, 127.775, 79.583
Angle α, β, γ (deg.)90.000, 106.883, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 1-deoxy-D-xylulose-5-phosphate synthase / 1-deoxyxylulose-5-phosphate synthase / DXP synthase / DXPS


Mass: 63685.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: dxs, Rv2682c, MTCY05A6.03c / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WNS3, 1-deoxy-D-xylulose-5-phosphate synthase

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Non-polymers , 6 types, 1334 molecules

#2: Chemical ChemComp-VMI / [(S)-1-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-5-[2-[oxidanyl(phosphonooxy)phosphoryl]oxyethyl]-1,3-thiazol-3-ium-2-yl]-1-oxidanyl-ethyl]-butoxy-phosphinic acid


Mass: 605.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H32N4O11P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1318 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 48.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 0.1 M MES-Imidazole pH 6.3, 10% PEG 8000 , 20% Ethylene-glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0333 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0333 Å / Relative weight: 1
ReflectionResolution: 1.6→48.94 Å / Num. obs: 155741 / % possible obs: 98.2 % / Redundancy: 7 % / CC1/2: 0.999 / Net I/σ(I): 15.8
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 7 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 7495 / CC1/2: 0.785 / % possible all: 95.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→48.94 Å / SU ML: 0.1496 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.1579
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1721 7892 5.07 %
Rwork0.1553 147664 -
obs0.1562 155556 97.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.99 Å2
Refinement stepCycle: LAST / Resolution: 1.6→48.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8214 0 129 1322 9665
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00928751
X-RAY DIFFRACTIONf_angle_d1.249611907
X-RAY DIFFRACTIONf_chiral_restr0.07581327
X-RAY DIFFRACTIONf_plane_restr0.01021580
X-RAY DIFFRACTIONf_dihedral_angle_d13.38893233
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.27622510.25384767X-RAY DIFFRACTION95.13
1.62-1.640.25252610.2254856X-RAY DIFFRACTION97.78
1.64-1.660.22652600.21434927X-RAY DIFFRACTION97.59
1.66-1.680.24692490.21054900X-RAY DIFFRACTION98.11
1.68-1.70.2332520.20794885X-RAY DIFFRACTION97.62
1.7-1.730.20432730.20284893X-RAY DIFFRACTION97.75
1.73-1.750.21022740.19214918X-RAY DIFFRACTION98.22
1.75-1.780.24542460.19084931X-RAY DIFFRACTION97.83
1.78-1.80.20692780.18424893X-RAY DIFFRACTION97.77
1.8-1.830.20752530.17474905X-RAY DIFFRACTION97.69
1.83-1.870.20682950.17544824X-RAY DIFFRACTION97.21
1.87-1.90.19592580.17774670X-RAY DIFFRACTION93.32
1.9-1.940.22822700.2064884X-RAY DIFFRACTION97.28
1.94-1.980.21272540.17694959X-RAY DIFFRACTION98.67
1.98-2.020.18052740.15754903X-RAY DIFFRACTION98.61
2.02-2.070.17772580.15434973X-RAY DIFFRACTION98.59
2.07-2.120.17372340.15644960X-RAY DIFFRACTION98.5
2.12-2.170.19232570.14744966X-RAY DIFFRACTION98.94
2.17-2.240.16512350.14874995X-RAY DIFFRACTION99.02
2.24-2.310.17212870.16654897X-RAY DIFFRACTION97.87
2.31-2.390.1632620.14384992X-RAY DIFFRACTION99
2.39-2.490.18042720.14434968X-RAY DIFFRACTION99.2
2.49-2.60.15622480.14754961X-RAY DIFFRACTION98.54
2.6-2.740.15982540.14744785X-RAY DIFFRACTION94.5
2.74-2.910.16692640.1485017X-RAY DIFFRACTION99.77
2.91-3.140.15512590.14425023X-RAY DIFFRACTION99.85
3.14-3.450.15582790.14315022X-RAY DIFFRACTION99.92
3.45-3.950.14332670.1335049X-RAY DIFFRACTION99.59
3.95-4.980.1362640.12494978X-RAY DIFFRACTION98.16

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