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- PDB-8v9i: 1-deoxy-D-xylulose 5-phosphate synthase (DXPS) from Deinococcus r... -

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Basic information

Entry
Database: PDB / ID: 8v9i
Title1-deoxy-D-xylulose 5-phosphate synthase (DXPS) from Deinococcus radiodurans with D-phenylalanine-derived triazole acetylphosphonate (D-PheTrAP) bound
Components1-deoxy-D-xylulose-5-phosphate synthase
KeywordsTRANSFERASE/INHIBITOR / 1-DEOXY-D-XYLULOSE 5-PHOSPHATE SYNTHASE / DXPS / THIAMINE DIPHOSPHATE / THIAMINE PYROPHOSPHATE / THDP / TPP / THE MEP PATHWAY / TRANSFERASE / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


1-deoxy-D-xylulose-5-phosphate synthase / 1-deoxy-D-xylulose 5-phosphate biosynthetic process / 1-deoxy-D-xylulose-5-phosphate synthase activity / chlorophyll biosynthetic process / thiamine biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / thiamine pyrophosphate binding / magnesium ion binding / cytosol
Similarity search - Function
Deoxyxylulose-5-phosphate synthase / 1-deoxy-D-xylulose-5-phosphate synthase / 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
: / 2-HYDROXY BUTANE-1,4-DIOL / 1-deoxy-D-xylulose-5-phosphate synthase
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.981 Å
AuthorsChen, P.Y.-T. / Drennan, C.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM126982 United States
CitationJournal: Acs Infect Dis. / Year: 2024
Title: Potent Inhibition of E. coli DXP Synthase by a gem -Diaryl Bisubstrate Analog.
Authors: Coco, L.B. / Toci, E.M. / Chen, P.Y. / Drennan, C.L. / Freel Meyers, C.L.
History
DepositionDec 8, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release

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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)141,8449
Polymers140,0592
Non-polymers1,7857
Water10,449580
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11340 Å2
ΔGint-102 kcal/mol
Surface area36570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.616, 125.321, 152.017
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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 / DXPS


Mass: 70029.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Gene: dxs, DR_1475 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9RUB5, 1-deoxy-D-xylulose-5-phosphate synthase

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Non-polymers , 5 types, 587 molecules

#2: Chemical ChemComp-A1AAN / 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-{(1S)-1-[(S)-(2-{1-[(1R)-1-carboxy-2-phenylethyl]-1H-1,2,3-triazol-4-yl}ethoxy)(hydroxy)phosphoryl]-1-hydroxyethyl}-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium


Mass: 792.608 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H37N7O13P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-BGQ / 2-HYDROXY BUTANE-1,4-DIOL


Mass: 105.112 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 580 / 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: 2.67 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop
Details: 0.056 M BES (Acros), 0.044 M triethanolamine, pH 7.5, 15% (w/v) PEG 3000 (Rigaku), 20% (v/v) 1,2,4-butanetriol (Alfa Aesar), 1% (w/v) nondetergent sulfobetaines (NDSB)-256 (Hampton), 25 mM L- ...Details: 0.056 M BES (Acros), 0.044 M triethanolamine, pH 7.5, 15% (w/v) PEG 3000 (Rigaku), 20% (v/v) 1,2,4-butanetriol (Alfa Aesar), 1% (w/v) nondetergent sulfobetaines (NDSB)-256 (Hampton), 25 mM L-arginine, 25 mM L-threonine, 25 mM L-histidine, and 25 mM trans-4-hydroxy-L-proline.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.981→66.597 Å / Num. obs: 103920 / % possible obs: 99.1 % / Redundancy: 6.3 % / Rsym value: 0.092 / Net I/σ(I): 19.4
Reflection shellResolution: 1.981→2.05 Å / Num. unique obs: 9553 / CC1/2: 0.808

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.981→66.597 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1812 5196 5.01 %
Rwork0.1601 --
obs0.1611 103784 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.981→66.597 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8845 0 113 580 9538
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039241
X-RAY DIFFRACTIONf_angle_d0.61812574
X-RAY DIFFRACTIONf_dihedral_angle_d17.725463
X-RAY DIFFRACTIONf_chiral_restr0.0451409
X-RAY DIFFRACTIONf_plane_restr0.0041640
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9814-2.00390.32811480.27312760X-RAY DIFFRACTION84
2.0039-2.02750.32531630.2613015X-RAY DIFFRACTION92
2.0275-2.05220.28591680.24383177X-RAY DIFFRACTION97
2.0522-2.07820.24931680.23543272X-RAY DIFFRACTION99
2.0782-2.10550.25731750.21663253X-RAY DIFFRACTION100
2.1055-2.13440.24581720.21223285X-RAY DIFFRACTION100
2.1344-2.16490.24591750.19523292X-RAY DIFFRACTION100
2.1649-2.19720.21541680.19023277X-RAY DIFFRACTION100
2.1972-2.23150.21211750.17933284X-RAY DIFFRACTION100
2.2315-2.26810.19831720.17683279X-RAY DIFFRACTION100
2.2681-2.30720.21741760.1743300X-RAY DIFFRACTION100
2.3072-2.34920.21241710.16763285X-RAY DIFFRACTION100
2.3492-2.39440.19841730.16193260X-RAY DIFFRACTION100
2.3944-2.44320.17941740.16153325X-RAY DIFFRACTION100
2.4432-2.49640.20471760.16193286X-RAY DIFFRACTION100
2.4964-2.55440.20051740.16183308X-RAY DIFFRACTION100
2.5544-2.61830.16581720.1583315X-RAY DIFFRACTION100
2.6183-2.68910.19191750.15883284X-RAY DIFFRACTION100
2.6891-2.76830.18841730.16233311X-RAY DIFFRACTION100
2.7683-2.85760.18661740.16053292X-RAY DIFFRACTION100
2.8576-2.95970.18371730.16513314X-RAY DIFFRACTION100
2.9597-3.07820.19561760.16313326X-RAY DIFFRACTION100
3.0782-3.21830.1851740.16543327X-RAY DIFFRACTION100
3.2183-3.3880.19691760.17093325X-RAY DIFFRACTION100
3.388-3.60030.18171770.16773365X-RAY DIFFRACTION100
3.6003-3.87820.17131730.14743344X-RAY DIFFRACTION100
3.8782-4.26840.13891800.12683363X-RAY DIFFRACTION100
4.2684-4.88590.13041780.12323390X-RAY DIFFRACTION100
4.8859-6.15510.16941790.14373416X-RAY DIFFRACTION100
6.1551-66.5970.14331880.15113558X-RAY DIFFRACTION99
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)
10.7482-0.0166-0.10191.7270.28460.93630.07190.02-0.00160.0083-0.07910.2742-0.024-0.17240.00690.17960.0229-0.03890.2090.00510.2318-15.5378-11.170236.4969
20.8120.189-0.07271.6635-0.0190.91910.0712-0.1489-0.06150.2793-0.0402-0.46770.0510.23020.01320.24570.0261-0.11260.2528-0.00230.353112.6185-10.976646.3261
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'

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