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- PDB-6qsi: Pseudomonas fluorescens Pf-5 thiamine diphosphate-dependent 4-hyd... -

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Basic information

Entry
Database: PDB / ID: 6qsi
TitlePseudomonas fluorescens Pf-5 thiamine diphosphate-dependent 4-hydroxybenzoylformate decarboxylase
ComponentsBenzoylformate decarboxylase
KeywordsOXIDOREDUCTASE / benzoylformate decarboxylase / thaimine diphosphate / Pseudomonas fluorescens Pf-5 / lignin degradation
Function / homology
Function and homology information


benzoylformate decarboxylase / benzoylformate decarboxylase activity / carboxylic acid metabolic process / thiamine pyrophosphate 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 (ThDP)-binding fold, Pyr/PP domains ...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 (ThDP)-binding fold, Pyr/PP domains / TPP-binding domain / Thiamin diphosphate-binding fold / DHS-like NAD/FAD-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
THIAMINE DIPHOSPHATE / Benzoylformate decarboxylase
Similarity search - Component
Biological speciesPseudomonas protegens Pf-5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsWilkinson, R.C. / Fulop, V.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/M025772/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/M003523/1 United Kingdom
CitationJournal: Biochemistry / Year: 2019
Title: Characterization of Thiamine Diphosphate-Dependent 4-Hydroxybenzoylformate Decarboxylase Enzymes fromRhodococcus jostiiRHA1 andPseudomonas fluorescensPf-5 Involved in Degradation of Aryl ...Title: Characterization of Thiamine Diphosphate-Dependent 4-Hydroxybenzoylformate Decarboxylase Enzymes fromRhodococcus jostiiRHA1 andPseudomonas fluorescensPf-5 Involved in Degradation of Aryl C2Lignin Degradation Fragments.
Authors: Wei, Z. / Wilkinson, R.C. / Rashid, G.M.M. / Brown, D. / Fulop, V. / Bugg, T.D.H.
History
DepositionFeb 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2020Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,0049
Polymers111,9212
Non-polymers1,0837
Water14,340796
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9940 Å2
ΔGint-84 kcal/mol
Surface area35910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.720, 130.720, 180.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1023-

HOH

21A-1104-

HOH

31B-1025-

HOH

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Components

#1: Protein Benzoylformate decarboxylase


Mass: 55960.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas protegens Pf-5 (bacteria) / Gene: mdlC, PFL_3478 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4KB02, benzoylformate decarboxylase
#2: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 796 / Source method: isolated from a natural source / Formula: H2O

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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: 2.92 Å3/Da / Density % sol: 49 % / Description: rod
Crystal growTemperature: 300 K / Method: vapor diffusion / pH: 4.6 / Details: 0.1 M sodium acetate pH 4.6, 2M sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.69→85 Å / Num. obs: 144852 / % possible obs: 99.6 % / Redundancy: 10.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.101 / Rrim(I) all: 0.105 / Net I/σ(I): 16.5
Reflection shellResolution: 1.69→1.78 Å / Rmerge(I) obs: 1.206 / Mean I/σ(I) obs: 2 / CC1/2: 0.786 / Rrim(I) all: 1.126 / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XDSdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.69→84.49 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.96 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.077 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17996 5756 4 %RANDOM
Rwork0.15927 ---
obs0.1601 139095 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.152 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.12 Å2
Refinement stepCycle: 1 / Resolution: 1.69→84.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7834 0 66 796 8696
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0198107
X-RAY DIFFRACTIONr_bond_other_d0.0020.027740
X-RAY DIFFRACTIONr_angle_refined_deg1.6541.97611097
X-RAY DIFFRACTIONr_angle_other_deg0.889317758
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.25151047
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.52723.252326
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.982151148
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4941558
X-RAY DIFFRACTIONr_chiral_restr0.0990.21232
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0219325
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021823
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.691→1.735 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 394 -
Rwork0.3 9775 -
obs--95.5 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.202-0.02350.00010.1905-0.05480.30750.02390.0429-0.0322-0.0412-0.0231-0.01450.07360.0139-0.00070.06990.0123-0.00410.0124-0.01260.083555.026144.692373.2436
20.0974-0.01050.01150.07230.04340.22080.0182-0.0253-0.01540.0271-0.0135-0.00810.0614-0.0153-0.00460.0465-0.016-0.00340.01120.01030.054848.053745.7773108.5147
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 526
2X-RAY DIFFRACTION2B2 - 525

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