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- PDB-6m2z: Crystal structure of a formolase, BFD variant M3 from Pseudomonas... -

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Basic information

Entry
Database: PDB / ID: 6m2z
TitleCrystal structure of a formolase, BFD variant M3 from Pseudomonas putida
ComponentsBenzoylformate decarboxylase
KeywordsBIOSYNTHETIC PROTEIN / benzoylformate 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: 2.35 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)56,8303
Polymers56,3811
Non-polymers4502
Water3,603200
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)227,32112
Polymers225,5234
Non-polymers1,7988
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area26290 Å2
ΔGint-190 kcal/mol
Surface area59960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.964, 101.385, 110.660
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-845-

HOH

21A-854-

HOH

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Components

#1: Protein Benzoylformate decarboxylase / BFDC


Mass: 56380.699 Da / Num. of mol.: 1 / Mutation: W86R, N87T, L109G, L110E, 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.: 200 / 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: 2.44 Å3/Da / Density % sol: 49.52 % / Mosaicity: 1.233 °
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M sodium acetate 4.6, 0.1 M sodium chloride, 12 % w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 26, 2019
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→25 Å / Num. obs: 23197 / % possible obs: 99.6 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.059 / Rrim(I) all: 0.149 / Χ2: 0.761 / Net I/σ(I): 6 / Num. measured all: 146939
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.35-2.435.80.76322460.8510.3390.8370.68699.5
2.43-2.536.30.64323040.9210.2770.7010.703100
2.53-2.656.50.52923190.9360.2240.5760.74100
2.65-2.796.50.42722920.9490.1820.4650.774100
2.79-2.966.40.30823150.9720.1310.3350.775100
2.96-3.196.50.22323080.9860.0940.2420.796100
3.19-3.516.60.1423260.9950.0590.1520.801100
3.51-4.016.20.10222830.9960.0440.1120.89597.9
4.01-5.056.40.06123630.9980.0260.0660.65499.7
5.05-256.10.06924410.9950.0310.0750.77899.3

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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: 2.35→24.5 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.918 / SU B: 9.467 / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.369 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1173 5.1 %RANDOM
Rwork0.1747 ---
obs0.1784 22004 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 116.71 Å2 / Biso mean: 38.732 Å2 / Biso min: 10.41 Å2
Baniso -1Baniso -2Baniso -3
1--4.52 Å20 Å20 Å2
2--4.56 Å20 Å2
3----0.04 Å2
Refinement stepCycle: final / Resolution: 2.35→24.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3937 0 27 200 4164
Biso mean--37.81 37.69 -
Num. residues----525
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134064
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173703
X-RAY DIFFRACTIONr_angle_refined_deg1.5321.6385548
X-RAY DIFFRACTIONr_angle_other_deg1.3051.5658593
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4975524
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.06722.412199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.64415601
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9591524
X-RAY DIFFRACTIONr_chiral_restr0.0660.2533
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024637
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02805
LS refinement shellResolution: 2.35→2.41 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 85 -
Rwork0.251 1552 -
all-1637 -
obs--99.15 %

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