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- PDB-9v6f: The crystal structure of a ThDP-dependent enzyme PpBFD -

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Basic information

Entry
Database: PDB / ID: 9v6f
TitleThe crystal structure of a ThDP-dependent enzyme PpBFD
ComponentsBenzoylformate decarboxylase
KeywordsBIOSYNTHETIC PROTEIN / thiamine-dependent photobiocatalysis
Function / homology
Function and homology information


benzoylformate decarboxylase / benzoylformate decarboxylase activity / (R)-mandelate catabolic process / acetolactate synthase activity / thiamine pyrophosphate binding / flavin adenine dinucleotide binding / magnesium ion binding
Similarity search - Function
Thiamine pyrophosphate enzyme / TPP-binding enzyme, conserved site / Thiamine pyrophosphate enzymes signature. / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / Thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, C-terminal TPP binding domain / Thiamin diphosphate-binding fold / DHS-like NAD/FAD-binding domain superfamily
Similarity search - Domain/homology
Benzoylformate decarboxylase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63875911505 Å
AuthorsHou, X.L. / Zhou, J.H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Catal / Year: 2026
Title: Enantioselective C(sp3)-C(sp3) bond formation by synergistic thiamine-dependent radical biocatalysis and photoredox catalysis
Authors: Chun, J. / Bao, Y. / Zhang, Q. / Hou, X. / Wu, Z. / Sun, H. / Xing, Z. / Chen, B. / Zhang, Z. / Zhao, Y. / Zhou, J. / Wang, B. / Huang, X.
History
DepositionMay 27, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2026Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Benzoylformate decarboxylase
B: Benzoylformate decarboxylase
C: Benzoylformate decarboxylase
D: Benzoylformate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,81151
Polymers226,7084
Non-polymers2,10347
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27470 Å2
ΔGint-369 kcal/mol
Surface area57990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.734, 114.370, 202.158
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

#1: Protein
Benzoylformate decarboxylase / BFD / BFDC


Mass: 56677.070 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: mdlC / Production host: Escherichia coli (E. coli) / References: UniProt: P20906, benzoylformate decarboxylase
#2: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.44 Å3/Da / Density % sol: 49.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10% w/v PEG 4000, 20% v/v glycerol 0.02 M of each alcohol 0.1 M MES/imidazole pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 17, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.63→49.78 Å / Num. obs: 64282 / % possible obs: 97.34 % / Redundancy: 13.2 % / Biso Wilson estimate: 44.0395329379 Å2 / CC1/2: 0.98 / Net I/σ(I): 16.6
Reflection shellResolution: 2.64→2.64 Å / Num. unique obs: 65100 / CC1/2: 0.98

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PHENIX1.12_2829refinement
HKL-3000data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.63875911505→49.7718701058 Å / SU ML: 0.319402785653 / Cross valid method: FREE R-VALUE / σ(F): 1.33843414211 / Phase error: 23.3919603273
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.230474226492 3190 4.96250894496 %
Rwork0.190631564137 61092 -
obs0.192588558857 64282 97.3423989582 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.388301967 Å2
Refinement stepCycle: LAST / Resolution: 2.63875911505→49.7718701058 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15313 0 117 246 15676
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036185502275315789
X-RAY DIFFRACTIONf_angle_d0.62438324850221554
X-RAY DIFFRACTIONf_chiral_restr0.04605677800372428
X-RAY DIFFRACTIONf_plane_restr0.004365363241922860
X-RAY DIFFRACTIONf_dihedral_angle_d2.7450194710712952
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6388-2.67810.296279989206750.2711694519511548X-RAY DIFFRACTION57.5124025514
2.6781-2.720.3031677590591600.2524345491242451X-RAY DIFFRACTION92.0662905501
2.72-2.76460.3093308328491370.2538342465412557X-RAY DIFFRACTION94.7257383966
2.7646-2.81220.3007093362091360.2526196306812657X-RAY DIFFRACTION98.4143763214
2.8122-2.86340.3288960713151320.2610531718132682X-RAY DIFFRACTION99.6458923513
2.8634-2.91840.3498212267591440.2594738367172678X-RAY DIFFRACTION99.8231340644
2.9184-2.9780.3252863526711430.2536076886082710X-RAY DIFFRACTION99.8949579832
2.978-3.04280.3331479985091370.25968045142678X-RAY DIFFRACTION99.9290024849
3.0428-3.11350.2768827920161510.24795520632692X-RAY DIFFRACTION100
3.1135-3.19140.2730112183531450.2381543851362718X-RAY DIFFRACTION99.8256624826
3.1914-3.27760.2518460557721480.2132664422262687X-RAY DIFFRACTION99.8942917548
3.2776-3.37410.234902046511400.2089972718252705X-RAY DIFFRACTION99.8946629213
3.3741-3.4830.2342608804941510.2084870500122692X-RAY DIFFRACTION99.6145760336
3.483-3.60740.2509743399421340.1957777904092692X-RAY DIFFRACTION99.4020400985
3.6074-3.75180.2550043890491320.1900611459432727X-RAY DIFFRACTION99.8951781971
3.7518-3.92250.2125088641631200.1705418779332777X-RAY DIFFRACTION99.9654934438
3.9225-4.12920.1955126177371260.1676826627542740X-RAY DIFFRACTION99.930264993
4.1292-4.38770.1872607581431550.1583159959182738X-RAY DIFFRACTION100
4.3877-4.72630.1939462221171410.1409358472332724X-RAY DIFFRACTION100
4.7263-5.20150.1881649852791450.1455690413152762X-RAY DIFFRACTION99.6571820363
5.2015-5.9530.1912363210521430.1690117562512766X-RAY DIFFRACTION99.452991453
5.953-7.49610.1924523315831400.1775356823952813X-RAY DIFFRACTION99.7972287935
7.4961-49.770.1867670152061550.1597641200442898X-RAY DIFFRACTION98.8025889968
Refinement TLS params.Method: refined / Origin x: 6.25678208841 Å / Origin y: 237.24407741 Å / Origin z: 222.321014575 Å
111213212223313233
T0.140023061103 Å2-0.0436019101324 Å20.0175319695933 Å2-0.123722964615 Å20.00948373844105 Å2--0.165435830264 Å2
L0.49232174524 °2-0.259955869832 °2-0.128091824388 °2-0.583595247044 °2-0.0824734659541 °2--0.673070401114 °2
S-0.00235790050019 Å °0.00991597713544 Å °-0.0558686780264 Å °-0.0661763777633 Å °-0.112253354245 Å °-0.095358312694 Å °0.128370765531 Å °0.0119330541287 Å °-0.0101162746625 Å °
Refinement TLS groupSelection details: all

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