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- PDB-6m2y: Crystal structure of a formolase, BFD variant M6 from Pseudomonas... -

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Basic information

Entry
Database: PDB / ID: 6m2y
TitleCrystal structure of a formolase, BFD variant M6 from Pseudomonas putida
ComponentsBenzoylformate decarboxylase
KeywordsBIOSYNTHETIC PROTEIN / decarboxylases
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: 2.1 Å
AuthorsWei, H.L. / Liu, W.D. / Li, T.Z. / Zhu, L.L.
CitationJournal: Green Chem / Year: 2020
Title: Totally atom-economical synthesis of lactic acid from formaldehyde: combined bio-carboligation and chemo-rearrangement without the isolation of intermediate.
Authors: Li, T. / Tang, Z. / Wei, H. / Tan, Z. / Liu, P. / Li, J. / Zheng, Y. / Lin, J. / Liu, W. / Jiang, H. / Liu, H. / Zhu, L. / Ma, Y.
History
DepositionMar 2, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Benzoylformate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9453
Polymers56,4961
Non-polymers4502
Water8,035446
1
A: Benzoylformate decarboxylase
hetero molecules

A: Benzoylformate decarboxylase
hetero molecules

A: Benzoylformate decarboxylase
hetero molecules

A: Benzoylformate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,78212
Polymers225,9834
Non-polymers1,7988
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area27840 Å2
ΔGint-203 kcal/mol
Surface area72030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.515, 106.674, 116.548
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-713-

HOH

21A-887-

HOH

31A-980-

HOH

41A-1048-

HOH

51A-1118-

HOH

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Components

#1: Protein Benzoylformate decarboxylase / BFDC


Mass: 56495.848 Da / Num. of mol.: 1 / Mutation: S26F, W86R, N87T, L109S, L110E, H281Y, A460M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: mdlC / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 trixb(DE3) / References: UniProt: P20906, benzoylformate decarboxylase
#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.: 446 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.85 Å3/Da / Density % sol: 56.8 % / Mosaicity: 0.579 °
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M acetate pH 4.5, 0.2 M NaCl,40% (v/v) PEG-300

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 9, 2019
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.06→25 Å / Num. obs: 39009 / % possible obs: 100 % / Redundancy: 12.4 % / Rmerge(I) obs: 0.245 / Rpim(I) all: 0.072 / Rrim(I) all: 0.255 / Χ2: 0.724 / Net I/σ(I): 3.5
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
2.1-2.189.41.02538690.8490.3421.0820.457
2.18-2.2610.80.89538420.9030.2810.9390.47
2.26-2.3612.80.7838510.9440.2260.8120.499
2.36-2.4913.20.60338560.960.1720.6270.534
2.49-2.6512.60.45238960.9760.1320.4710.558
2.65-2.8513.10.3238700.9860.0920.3330.65
2.85-3.1413.50.23738830.990.0670.2460.701
3.14-3.5912.70.16139160.9940.0470.1680.924
3.59-4.5213.60.10939450.9960.0310.1141.171
4.52-2512.50.08440810.9960.0250.0881.11

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A50

6a50


Resolution: 2.1→24.6 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.919 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1891 1848 4.9 %RANDOM
Rwork0.154 ---
obs0.1558 36101 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.05 Å2 / Biso mean: 16.587 Å2 / Biso min: 3.89 Å2
Baniso -1Baniso -2Baniso -3
1--1.51 Å20 Å20 Å2
2--1.47 Å20 Å2
3---0.03 Å2
Refinement stepCycle: final / Resolution: 2.1→24.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3954 0 27 446 4427
Biso mean--20.41 28.18 -
Num. residues----526
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0134082
X-RAY DIFFRACTIONr_bond_other_d00.0173720
X-RAY DIFFRACTIONr_angle_refined_deg2.2541.6385572
X-RAY DIFFRACTIONr_angle_other_deg1.2191.5648631
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.415525
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.32222.4200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.3515605
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.51524
X-RAY DIFFRACTIONr_chiral_restr0.0860.2535
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024653
X-RAY DIFFRACTIONr_gen_planes_other00.02813
LS refinement shellResolution: 2.1→2.154 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 113 -
Rwork0.213 2654 -
all-2767 -
obs--100 %

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