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

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Basic information

Entry
Database: PDB / ID: 8xod
TitleThDP-dependent HKA synthase
ComponentsBbmA-G484F complex with CBOA
KeywordsBIOSYNTHETIC PROTEIN / ThDP-dependent HKA synthase / mutant of BbmA
Function / homology: / ADENOSINE-5'-DIPHOSPHATE / THIAMINE DIPHOSPHATE
Function and homology information
Biological speciesBrevibacillus (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
DepositionJan 1, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 1, 2025Provider: 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: BbmA-G484F complex with CBOA
B: BbmA-G484F complex with CBOA
C: BbmA-G484F complex with CBOA
D: BbmA-G484F complex with CBOA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)253,63815
Polymers249,9034
Non-polymers3,73511
Water1267
1
A: BbmA-G484F complex with CBOA
D: BbmA-G484F complex with CBOA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,8738
Polymers124,9522
Non-polymers1,9226
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8460 Å2
ΔGint-67 kcal/mol
Surface area33730 Å2
MethodPISA
2
B: BbmA-G484F complex with CBOA
C: BbmA-G484F complex with CBOA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,7657
Polymers124,9522
Non-polymers1,8135
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9300 Å2
ΔGint-77 kcal/mol
Surface area33760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.935, 116.695, 201.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
BbmA-G484F complex with CBOA


Mass: 62475.793 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevibacillus (bacteria)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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Non-polymers , 5 types, 18 molecules

#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-A1LX0 / 2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-2-[(~{R})-cyclobutyl(oxidanyl)methyl]-4-methyl-1,3-thiazol-5-yl]ethyl phosphono hydrogen phosphate


Mass: 509.431 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H27N4O8P2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N4O7P2S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.3 Å3/Da / Density % sol: 46.58 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 24% polyethlene glycol 400, 0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate, pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.75→24.94 Å / Num. obs: 59507 / % possible obs: 99.8 % / Redundancy: 9 % / Rmerge(I) obs: 0.146 / Net I/σ(I): 8.9
Reflection shellResolution: 2.75→2.83 Å / Rmerge(I) obs: 0.619 / Num. unique obs: 4562

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Processing

Software
NameVersionClassification
PHENIX1.1.17.3360refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2.75→24.94 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2864 --
Rwork0.203 --
obs-59507 99.8 %
Refinement stepCycle: LAST / Resolution: 2.75→24.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15846 0 233 7 16086
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013716443
X-RAY DIFFRACTIONf_angle_d1.489122395
X-RAY DIFFRACTIONf_chiral_restr0.09352565
X-RAY DIFFRACTIONf_plane_restr0.00922861
X-RAY DIFFRACTIONf_dihedral_angle_d22.89035923

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