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- PDB-8bzx: 1-deoxy-D-xylulose 5-phosphate synthase from Klebsiella pneumonia... -

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Basic information

Entry
Database: PDB / ID: 8bzx
Title1-deoxy-D-xylulose 5-phosphate synthase from Klebsiella pneumoniae (kpDXPS),co-crystal with thiamine monophosphate analog
Components1-deoxy-D-xylulose-5-phosphate synthase
KeywordsTRANSFERASE / 1-deoxy-D-xylulose 5-phosphate synthase / Klebsiella pneumoniae / thiamine monophosphate
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 biosynthetic process / terpenoid biosynthetic process / thiamine pyrophosphate binding / magnesium ion binding
Similarity search - Function
Deoxyxylulose-5-phosphate synthase / 1-deoxy-D-xylulose-5-phosphate synthase / Transketolase signature 1. / Transketolase binding site / Transketolase signature 2. / Transketolase, N-terminal / 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, N-terminal / 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
Chem-SW6 / 1-deoxy-D-xylulose-5-phosphate synthase / 1-deoxy-D-xylulose-5-phosphate synthase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsHamid, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
Helmholtz Association Germany
CitationJournal: Bioorg.Chem. / Year: 2023
Title: Design of thiamine analogues for inhibition of thiamine diphosphate (ThDP)-dependent enzymes: Systematic investigation through Scaffold-Hopping and C2-Functionalisation.
Authors: Chan, A.H.Y. / Ho, T.C.S. / Irfan, R. / Hamid, R.A.A. / Rudge, E.S. / Iqbal, A. / Turner, A. / Hirsch, A.K.H. / Leeper, F.J.
History
DepositionDec 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)127,3807
Polymers126,5082
Non-polymers8725
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9060 Å2
ΔGint-83 kcal/mol
Surface area34500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.249, 150.969, 142.145
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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


Mass: 63254.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: dxs_3, dxs, ETE82_13950 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A486V6R5, UniProt: A0A483FYN3, 1-deoxy-D-xylulose-5-phosphate synthase
#2: Chemical ChemComp-SW6 / 2-[4-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-3-methyl-5-propanoyl-thiophen-2-yl]ethyl dihydrogen phosphate


Mass: 399.402 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H22N3O5PS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O
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: 2.53 Å3/Da / Density % sol: 51.35 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion / pH: 7.5 / Details: 200 mM MgCl2, 100 mM HEPES pH 7.5 and 18% PEG8000

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Data collection

DiffractionMean temperature: 273.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Nov 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 2.05→46.79 Å / Num. obs: 80381 / % possible obs: 99.84 % / Redundancy: 2.1 % / Biso Wilson estimate: 34.97 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 3
Reflection shellResolution: 2.05→2.123 Å / Rmerge(I) obs: 0.238 / Mean I/σ(I) obs: 7.2 / Num. unique obs: 7953

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHASER1.20.1_4487phasing
PHASER1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→46.79 Å / SU ML: 0.3124 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.0892
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2641 3953 4.92 %
Rwork0.2171 76321 -
obs0.2194 80274 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.74 Å2
Refinement stepCycle: LAST / Resolution: 2.05→46.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8494 0 55 230 8779
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00718725
X-RAY DIFFRACTIONf_angle_d0.818111834
X-RAY DIFFRACTIONf_chiral_restr0.05211323
X-RAY DIFFRACTIONf_plane_restr0.00831539
X-RAY DIFFRACTIONf_dihedral_angle_d6.57621212
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.080.45781380.45712662X-RAY DIFFRACTION98.73
2.08-2.10.43561500.41572680X-RAY DIFFRACTION99.65
2.1-2.130.42251270.37912731X-RAY DIFFRACTION99.93
2.13-2.160.42851400.36372685X-RAY DIFFRACTION99.72
2.16-2.190.38641440.34542712X-RAY DIFFRACTION99.69
2.19-2.220.34131280.32322689X-RAY DIFFRACTION99.82
2.22-2.260.38061260.30772725X-RAY DIFFRACTION99.86
2.26-2.290.34251730.29482693X-RAY DIFFRACTION99.93
2.29-2.330.35211260.29122691X-RAY DIFFRACTION99.89
2.33-2.380.34471370.27732698X-RAY DIFFRACTION99.93
2.38-2.420.33751410.26762714X-RAY DIFFRACTION99.9
2.42-2.470.29931240.26032732X-RAY DIFFRACTION99.9
2.47-2.520.31571260.24942729X-RAY DIFFRACTION99.79
2.52-2.580.35621430.26042701X-RAY DIFFRACTION100
2.58-2.650.32151470.26022702X-RAY DIFFRACTION99.86
2.65-2.720.34731540.24222704X-RAY DIFFRACTION99.93
2.72-2.80.24151500.23132721X-RAY DIFFRACTION100
2.8-2.890.29311680.21232677X-RAY DIFFRACTION99.89
2.89-2.990.23081420.21282731X-RAY DIFFRACTION99.93
2.99-3.110.26351470.21542725X-RAY DIFFRACTION100
3.11-3.250.30151470.20932719X-RAY DIFFRACTION99.93
3.25-3.430.25991230.21312775X-RAY DIFFRACTION100
3.43-3.640.26171270.19652741X-RAY DIFFRACTION99.86
3.64-3.920.21471420.18192748X-RAY DIFFRACTION100
3.92-4.320.19691410.16462761X-RAY DIFFRACTION100
4.32-4.940.19431500.15482763X-RAY DIFFRACTION100
4.94-6.220.20341510.1742790X-RAY DIFFRACTION100
6.22-46.790.21111410.17072922X-RAY DIFFRACTION99.67
Refinement TLS params.Method: refined / Origin x: 40.531249333 Å / Origin y: 34.7358288456 Å / Origin z: 76.2107094437 Å
111213212223313233
T0.232982986448 Å2-0.0464779661808 Å2-0.00425175341566 Å2-0.572452271358 Å2-0.0102001223328 Å2--0.268869273665 Å2
L0.831536214721 °2-0.00422160175566 °2-0.0424538996783 °2-0.302733271579 °2-0.00048335381453 °2--0.928261813382 °2
S-0.0164860906599 Å °-0.069488858847 Å °-0.0369572322697 Å °0.037483445115 Å °0.011286861492 Å °0.00157201859838 Å °0.0287839705705 Å °-0.0153061794454 Å °0.00120628470685 Å °
Refinement TLS groupSelection details: all

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