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- PDB-8xbq: Crystal structure of activity improved formolase variant K1 -

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Basic information

Entry
Database: PDB / ID: 8xbq
TitleCrystal structure of activity improved formolase variant K1
ComponentsBenzoylformate decarboxylase-K2
KeywordsBIOSYNTHETIC PROTEIN / formolase
Function / homology
Function and homology information


benzoylformate decarboxylase / benzoylformate decarboxylase activity / 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
THIAMINE DIPHOSPHATE / Benzoylformate decarboxylase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsWei, H.L. / Cheng, Y.Y. / Tang, Z.J. / Tan, Z.J. / Liu, W.D. / Zhu, L.L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Acs Catalysis / Year: 2025
Title: Helix Zipper Regulating Formolase Activity.
Authors: Tan, Z.J. / Tang, Z.J. / Wei, H.L. / Zhang, R. / Sun, L. / Liu, W.D. / Liu, H.F. / Zhu, L.L. / Ma, Y.H.
History
DepositionDec 6, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2025Group: Database references / Structure summary / Category: citation / citation_author / struct
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 / _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Benzoylformate decarboxylase-K2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8863
Polymers56,4371
Non-polymers4502
Water6,575365
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.271, 99.376, 110.092
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-850-

HOH

21A-857-

HOH

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Components

#1: Protein Benzoylformate decarboxylase-K2 / BFD-K2


Mass: 56436.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: mdlC
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P20906
#2: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 2.38 Å3/Da / Density % sol: 48.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium citrate 5.5, 20 % w/v PEG 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.05→25 Å / Num. obs: 34208 / % possible obs: 99.5 % / Redundancy: 6.3 % / CC1/2: 0.987 / Net I/σ(I): 13.4
Reflection shellResolution: 2.05→2.12 Å / Mean I/σ(I) obs: 3.12 / Num. unique obs: 3407 / CC1/2: 0.889 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→24.6 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.912 / SU B: 4.984 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.199 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24141 1719 5 %RANDOM
Rwork0.17781 ---
obs0.18105 32454 98.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.749 Å2
Baniso -1Baniso -2Baniso -3
1--3.04 Å20 Å20 Å2
2--2.39 Å20 Å2
3---0.65 Å2
Refinement stepCycle: 1 / Resolution: 2.05→24.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3934 0 27 365 4326
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134067
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173715
X-RAY DIFFRACTIONr_angle_refined_deg1.5761.6395548
X-RAY DIFFRACTIONr_angle_other_deg1.3771.5658616
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.2245524
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.10922.289201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.34715606
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1691525
X-RAY DIFFRACTIONr_chiral_restr0.080.2533
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024641
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02812
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_it1.9072.7952099
X-RAY DIFFRACTIONr_mcbond_other1.9062.7942098
X-RAY DIFFRACTIONr_mcangle_it2.6114.1832622
X-RAY DIFFRACTIONr_mcangle_other2.6114.1842623
X-RAY DIFFRACTIONr_scbond_it2.6073.0821967
X-RAY DIFFRACTIONr_scbond_other2.5593.0831957
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8244.5122927
X-RAY DIFFRACTIONr_long_range_B_refined5.60454.12217656
X-RAY DIFFRACTIONr_long_range_B_other5.52953.9717412
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.093 Å
RfactorNum. reflection% reflection
Rfree0.285 110 -
Rwork0.235 2103 -
obs--88.63 %

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