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- PDB-8s65: 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR) as target f... -

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Basic information

Entry
Database: PDB / ID: 8s65
Title1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR) as target for anti Toxoplasma gondii compounds: crystal structure, biochemical characterization and biological evaluation of inhibitors
Components1-deoxy-D-xylulose-5-phosphate reductoisomerase
KeywordsSTRUCTURAL PROTEIN / 1-deoxy-D-xylulose-5-phosphate reductoisomerase
Function / homology
Function and homology information


isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway involved in terpenoid biosynthetic process / 1-deoxy-D-xylulose-5-phosphate reductoisomerase / 1-deoxy-D-xylulose-5-phosphate reductoisomerase activity / NADPH binding / isomerase activity / manganese ion binding
Similarity search - Function
1-deoxy-D-xylulose 5-phosphate reductoisomerase / 1-deoxy-D-xylulose 5-phosphate reductoisomerase, N-terminal / 1-deoxy-D-xylulose 5-phosphate reductoisomerase, C-terminal / DXP reductoisomerase C-terminal domain / DXP reductoisomerase, C-terminal domain superfamily / 1-deoxy-D-xylulose 5-phosphate reductoisomerase / 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal domain / DXP reductoisomerase C-terminal domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
3-[FORMYL(HYDROXY)AMINO]PROPYLPHOSPHONIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 1-deoxy-D-xylulose-5-phosphate reductoisomerase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SOLUTION SCATTERING / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsMazzone, F. / Hoeppner, A. / Reiners, J. / Applegate, V. / Abdullaziz, M. / Gottstein, J. / Wesemann, M. / Kurz, T. / Smits, S.H. / Pfeffer, K.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)270650915 Germany
German Research Foundation (DFG)417919780 Germany
CitationJournal: Biochem.J. / Year: 2024
Title: 1-Deoxy-d-xylulose 5-phosphate reductoisomerase as target for anti Toxoplasma gondii agents: crystal structure, biochemical characterization and biological evaluation of inhibitors.
Authors: Mazzone, F. / Hoeppner, A. / Reiners, J. / Gertzen, C.G.W. / Applegate, V. / Abdullaziz, M.A. / Gottstein, J. / Degrandi, D. / Wesemann, M. / Kurz, T. / Smits, S.H.J. / Pfeffer, K.
History
DepositionFeb 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)105,79612
Polymers103,7752
Non-polymers2,02110
Water1629
1
A: 1-deoxy-D-xylulose-5-phosphate reductoisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9237
Polymers51,8881
Non-polymers1,0356
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 1-deoxy-D-xylulose-5-phosphate reductoisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8745
Polymers51,8881
Non-polymers9864
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)159.524, 159.524, 75.873
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGARGARG(chain 'A' and (resid 25 through 465 or resid 467 through 472 or resid 501 through 504))AA25 - 18225 - 182
12LYSLYSALAALA(chain 'A' and (resid 25 through 465 or resid 467 through 472 or resid 501 through 504))AA221 - 464221 - 464
13ALAALAARGARG(chain 'A' and (resid 25 through 465 or resid 467 through 472 or resid 501 through 504))AA467 - 471467 - 471
14NAPNAPNAPNAP(chain 'A' and (resid 25 through 465 or resid 467 through 472 or resid 501 through 504))AC501
15FOMFOMFOMFOM(chain 'A' and (resid 25 through 465 or resid 467 through 472 or resid 501 through 504))AD502
26ARGARGARGARG(chain 'B' and (resid 25 through 182 or resid 221...BB25 - 18225 - 182
27LYSLYSALAALA(chain 'B' and (resid 25 through 182 or resid 221...BB221 - 464221 - 464
28ALAALAARGARG(chain 'B' and (resid 25 through 182 or resid 221...BB467 - 471467 - 471
29NAPNAPFOMFOM(chain 'B' and (resid 25 through 182 or resid 221...BI - J501 - 502

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 1-deoxy-D-xylulose-5-phosphate reductoisomerase


Mass: 51887.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: TGME49_214850 / Production host: Escherichia coli (E. coli)
References: UniProt: S8ESX0, 1-deoxy-D-xylulose-5-phosphate reductoisomerase

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Non-polymers , 5 types, 19 molecules

#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FOM / 3-[FORMYL(HYDROXY)AMINO]PROPYLPHOSPHONIC ACID / FOSMIDOMYCIN


Mass: 183.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10NO5P / Comment: antibiotic*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 9 / 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

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
SOLUTION SCATTERING

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.2 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop
Details: 200 mM Na citrate tribasic, 27% PEG smear low, 150 mM HEPES pH 7.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.918402 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918402 Å / Relative weight: 1
ReflectionResolution: 2.56→66.5 Å / Num. obs: 35431 / % possible obs: 99 % / Redundancy: 1.9 % / Biso Wilson estimate: 65.79 Å2 / CC1/2: 0.999 / Net I/σ(I): 11.5
Reflection shellResolution: 2.56→2.61 Å / Mean I/σ(I) obs: 1.17 / Num. unique obs: 3503 / CC1/2: 0.76

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.56→66.5 Å / SU ML: 0.3427 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.9303
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2254 2004 5.66 %
Rwork0.1937 33427 -
obs0.1956 35431 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 81.21 Å2
Refinement stepCycle: LAST / Resolution: 2.56→66.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6275 0 124 9 6408
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02166532
X-RAY DIFFRACTIONf_angle_d2.02618877
X-RAY DIFFRACTIONf_chiral_restr0.07781002
X-RAY DIFFRACTIONf_plane_restr0.01281148
X-RAY DIFFRACTIONf_dihedral_angle_d25.4979940
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.56-2.620.39641400.32852378X-RAY DIFFRACTION98.63
2.62-2.690.37211410.2962354X-RAY DIFFRACTION99.52
2.69-2.770.35241440.27642386X-RAY DIFFRACTION99.65
2.77-2.860.31591460.25392397X-RAY DIFFRACTION99.57
2.86-2.960.31461410.24232376X-RAY DIFFRACTION99.64
2.96-3.080.28491430.23222392X-RAY DIFFRACTION99.45
3.08-3.220.29461440.23222392X-RAY DIFFRACTION99.37
3.22-3.390.27281390.22252405X-RAY DIFFRACTION99.45
3.39-3.60.23991450.1982397X-RAY DIFFRACTION99.22
3.6-3.880.21891420.18342366X-RAY DIFFRACTION99.44
3.88-4.270.19371440.16832391X-RAY DIFFRACTION98.48
4.27-4.890.18651460.1482396X-RAY DIFFRACTION98.8
4.89-6.160.19771430.18742396X-RAY DIFFRACTION98.56
6.16-66.50.18081460.1752401X-RAY DIFFRACTION96.22

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