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- PDB-9kpq: A ThDP-dependent enzyme belonging to the 1-deoxy-D-xylulose-5-pho... -

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Basic information

Entry
Database: PDB / ID: 9kpq
TitleA ThDP-dependent enzyme belonging to the 1-deoxy-D-xylulose-5-phosphate synthase (DXPS)-like subfamily
Components1-deoxy-D-xylulose-5-phosphate synthase
KeywordsBIOSYNTHETIC PROTEIN / BoADS is a ThDP-dependent enzyme belonging to the 1-deoxy-D-xylulose-5-phosphate synthase (DXPS)-like subfamily.
Function / homology
Function and homology information


1-deoxy-D-xylulose-5-phosphate synthase / : / 1-deoxy-D-xylulose-5-phosphate synthase activity / thiamine biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / metal ion binding / cytosol
Similarity search - Function
Deoxyxylulose-5-phosphate synthase / 1-deoxy-D-xylulose-5-phosphate synthase / 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
THIAMINE DIPHOSPHATE / 1-deoxy-D-xylulose-5-phosphate synthase
Similarity search - Component
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsXing, B.Y. / Ma, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31925021, 82130022, 92357305, 82341226, 82422017, 82288102, 82370812, 92149306, 81921001, 82171627, 82325046 China
Citation
Journal: Cell / Year: 2025
Title: Identification of gut microbial bile acid metabolic enzymes via an AI-assisted pipeline.
Authors: Ding, Y. / Luo, X. / Guo, J. / Xing, B. / Lin, H. / Ma, H. / Wang, Y. / Li, M. / Ye, C. / Yan, S. / Lin, K. / Zhang, J. / Zhuo, Y. / Nie, Q. / Yang, D. / Zhang, Z. / Pang, Y. / Wang, K. / ...Authors: Ding, Y. / Luo, X. / Guo, J. / Xing, B. / Lin, H. / Ma, H. / Wang, Y. / Li, M. / Ye, C. / Yan, S. / Lin, K. / Zhang, J. / Zhuo, Y. / Nie, Q. / Yang, D. / Zhang, Z. / Pang, Y. / Wang, K. / Ma, M. / Lai, L. / Jiang, C.
#1: Journal: Commun Biol / Year: 2025
Title: Structural basis for Salmonella infection by two Microviridae phages.
Authors: Wanlong Hu / Zhengjie Liu / Yuming Wei / Qucheng Bian / Weiqi Lan / Chongzheng Fan / Jiaoyang Song / Qianqian Sun / Xiaojie Zhang / Yuqing Liu / Yan Gao / Yibao Chen /
Abstract: The global resurgence of multidrug-resistant Salmonella species, responsible for millions of annual infections, underscores the urgent need for alternative antimicrobial strategies, such as phage ...The global resurgence of multidrug-resistant Salmonella species, responsible for millions of annual infections, underscores the urgent need for alternative antimicrobial strategies, such as phage therapy. Microviridae phages offer a promising model for studying phage-host interactions with their unique structural and infection mechanisms. Here, we identify two Microviridae phages, PJNS001 and PJNS002, with different host receptor dependencies, and determine their cryo-EM structures at 2.68 Å and 2.59 Å resolution, respectively. These icosahedral capsids with T = 1 symmetry exhibit a unique vertex reinforcement mechanism, stabilizing the viral assembly. The specific pentameric adaptations, coupled with DNA binding protein engagements and thermodynamic constraints, collectively preclude the formation of hybrid virions. Structural analysis and in situ visualization reveal spike protein features and host-attachment intermediates, informing host specificity. Together, these findings advance our understanding of Microviridae infection mechanisms and provide a structural framework for rational phage design against antibiotic-resistant pathogens.
#2: Journal: Cell / Year: 2025
Title: Identification of gut microbial bile acid metabolic enzymes via an AI-assisted pipeline.
Authors: Ding, Y. / Luo, X. / Guo, J. / Xing, B. / Lin, H. / Ma, H. / Wang, Y. / Li, M. / Ye, C. / Yan, S. / Lin, K. / Zhang, J. / Zhuo, Y. / Nie, Q. / Yang, D. / Zhang, Z. / Pang, Y. / Wang, K. / ...Authors: Ding, Y. / Luo, X. / Guo, J. / Xing, B. / Lin, H. / Ma, H. / Wang, Y. / Li, M. / Ye, C. / Yan, S. / Lin, K. / Zhang, J. / Zhuo, Y. / Nie, Q. / Yang, D. / Zhang, Z. / Pang, Y. / Wang, K. / Ma, M. / Lai, L. / Jiang, C.
History
DepositionNov 23, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 20, 2025Provider: 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)131,4666
Polymers130,5672
Non-polymers8994
Water6,215345
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10360 Å2
ΔGint-81 kcal/mol
Surface area38830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.654, 71.787, 118.447
Angle α, β, γ (deg.)90.00, 97.05, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 65283.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus (bacteria) / Gene: DHW41_08530, DWY24_16555, R4E93_11875 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A1Y4PZZ8, 1-deoxy-D-xylulose-5-phosphate synthase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.37 Å3/Da / Density % sol: 48.01 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Sodium malonate pH 6.0, 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97954 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 30, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97954 Å / Relative weight: 1
ReflectionResolution: 2.42→48.66 Å / Num. obs: 46470 / % possible obs: 99.77 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.1022 / Net I/σ(I): 9.2
Reflection shellResolution: 2.42→2.51 Å / Rmerge(I) obs: 0.4262 / Mean I/σ(I) obs: 3.45 / Num. unique obs: 4553

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACTdata extraction
PHASESphasing
PHENIX1.17refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.42→48.66 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.885 / SU B: 9.752 / SU ML: 0.222 / Cross valid method: THROUGHOUT / ESU R: 0.606 / ESU R Free: 0.294 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25664 2325 5 %RANDOM
Rwork0.19225 ---
obs0.1955 44157 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.793 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20.01 Å2
2--0.01 Å20 Å2
3---0.07 Å2
Refinement stepCycle: 1 / Resolution: 2.42→48.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9138 0 54 345 9537
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0139374
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178695
X-RAY DIFFRACTIONr_angle_refined_deg1.7811.64512713
X-RAY DIFFRACTIONr_angle_other_deg1.2821.57820054
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.72351166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.97723.951486
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.393151581
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1491538
X-RAY DIFFRACTIONr_chiral_restr0.080.21212
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0210726
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022072
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9612.414670
X-RAY DIFFRACTIONr_mcbond_other1.9612.4094669
X-RAY DIFFRACTIONr_mcangle_it2.9993.615834
X-RAY DIFFRACTIONr_mcangle_other2.9993.6115835
X-RAY DIFFRACTIONr_scbond_it2.3632.6624703
X-RAY DIFFRACTIONr_scbond_other2.2932.6414650
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6873.8636800
X-RAY DIFFRACTIONr_long_range_B_refined5.46728.45310459
X-RAY DIFFRACTIONr_long_range_B_other5.36628.34110319
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.42→2.482 Å
RfactorNum. reflection% reflection
Rfree0.326 168 -
Rwork0.256 3173 -
obs--97.55 %

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