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- PDB-8x3z: ThDP-dependent HKA synthase -

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Basic information

Entry
Database: PDB / ID: 8x3z
TitleThDP-dependent HKA synthase
ComponentsCsmA
KeywordsBIOSYNTHETIC PROTEIN / ThDP-dependent enzyme / CsmA
Function / homologyADENOSINE-5'-DIPHOSPHATE / THIAMINE DIPHOSPHATE
Function and homology information
Biological speciesChryseomicrobium sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsYu, J.H. / Liu, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat.Chem. / Year: 2025
Title: Structural insights into two thiamine diphosphate-dependent enzymes and their synthetic applications in carbon-carbon linkage reactions.
Authors: Liu, T. / Wang, G. / Yu, J. / Li, M. / Peng, T. / Wang, J. / Li, H. / Su, X.D. / Jiang, C. / Ye, M. / Yang, D. / Ma, M.
History
DepositionNov 14, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 4, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 16, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CsmA
B: CsmA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,7246
Polymers118,4202
Non-polymers1,3044
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7990 Å2
ΔGint-71 kcal/mol
Surface area32810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.916, 129.734, 220.675
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein CsmA


Mass: 59210.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chryseomicrobium sp. (bacteria)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N4O7P2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.65 Å3/Da / Density % sol: 66.3 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris Propane-HCl with 1.0 M Ammonium Citrate Tribasic, pH 7.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.75→48.65 Å / Num. obs: 45049 / % possible obs: 100 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 20.4
Reflection shellResolution: 2.75→2.85 Å / Rmerge(I) obs: 0.597 / Num. unique obs: 4352

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2.75→45.98 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.219 --
Rwork0.1722 --
obs-45049 100 %
Refinement stepCycle: LAST / Resolution: 2.75→45.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7634 0 81 80 7795
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01517863
X-RAY DIFFRACTIONf_angle_d1.372110730
X-RAY DIFFRACTIONf_chiral_restr0.08621262
X-RAY DIFFRACTIONf_plane_restr0.00831394
X-RAY DIFFRACTIONf_dihedral_angle_d25.00942824

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