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- PDB-8y8m: Crystal structure of a benzaldehyde lyase mutant M3 from Herbicon... -

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Basic information

Entry
Database: PDB / ID: 8y8m
TitleCrystal structure of a benzaldehyde lyase mutant M3 from Herbiconiux sp. SALV-R1
ComponentsThiamine pyrophosphate-binding protein
KeywordsLYASE / benzaldehyde / mutant
Function / homology
Function and homology information


acetolactate synthase complex / acetolactate synthase activity / L-valine biosynthetic process / isoleucine biosynthetic process / thiamine pyrophosphate binding / flavin adenine dinucleotide binding / magnesium ion binding
Similarity search - Function
Thiamine pyrophosphate enzyme / 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
DI(HYDROXYETHYL)ETHER / THIAMINE DIPHOSPHATE / Thiamine pyrophosphate-binding protein
Similarity search - Component
Biological speciesHerbiconiux sp. SALV-R1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsLi, Y. / Zhang, Y.F. / Chen, Y.Y. / Liu, W.D. / Yao, P.Y. / Wu, Q.Q. / Zhu, D.M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Acs Catalysis / Year: 2024
Title: Manipulating Activity and Chemoselectivity of a Benzaldehyde Lyase for Efficient Synthesis of alpha-Hydroxymethyl Ketones and One-Pot Enantio-Complementary Conversion to 1,2-Diols
Authors: Zhang, Y. / Li, Y. / Chen, Y. / Liu, W. / Zhao, Q. / Feng, J. / Yao, P. / Wu, Q. / Zhu, D.
History
DepositionFeb 6, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thiamine pyrophosphate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6779
Polymers58,4121
Non-polymers1,2658
Water5,224290
1
A: Thiamine pyrophosphate-binding protein
hetero molecules

A: Thiamine pyrophosphate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,35318
Polymers116,8242
Non-polymers2,52916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Buried area9970 Å2
ΔGint-43 kcal/mol
Surface area36550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.020, 151.020, 110.745
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-914-

HOH

21A-966-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Thiamine pyrophosphate-binding protein


Mass: 58411.934 Da / Num. of mol.: 1 / Mutation: A27I, V29I, G417S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Herbiconiux sp. SALV-R1 (bacteria) / Gene: HL652_19860
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A6M5J4S0

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Non-polymers , 5 types, 298 molecules

#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


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


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


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.13 Å3/Da / Density % sol: 60.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.05M CaCl, 0.1M MES pH 6.0, 45% PEG 200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17UM / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 14, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.98→49.43 Å / Num. obs: 52172 / % possible obs: 100 % / Redundancy: 1.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.05 / Rrim(I) all: 0.071 / Χ2: 0.77 / Net I/σ(I): 7.5 / Num. measured all: 98463
Reflection shellResolution: 1.98→2.03 Å / Redundancy: 1.9 % / Num. unique obs: 3625 / CC1/2: 0.447 / Χ2: 0.87

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→49.43 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.28 / Phase error: 22.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.209 2604 5 %
Rwork0.18 --
obs0.181 52043 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.98→49.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4058 0 79 290 4427
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0174218
X-RAY DIFFRACTIONf_angle_d1.545751
X-RAY DIFFRACTIONf_dihedral_angle_d11.265655
X-RAY DIFFRACTIONf_chiral_restr0.105676
X-RAY DIFFRACTIONf_plane_restr0.027752
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.050.34722550.33574866X-RAY DIFFRACTION100
2.05-2.130.30892560.28284845X-RAY DIFFRACTION100
2.13-2.230.27032570.23574886X-RAY DIFFRACTION100
2.23-2.350.24382570.2064866X-RAY DIFFRACTION100
2.35-2.490.21262560.17874888X-RAY DIFFRACTION100
2.49-2.690.21552580.17074887X-RAY DIFFRACTION100
2.69-2.960.20412600.16444936X-RAY DIFFRACTION100
2.96-3.390.21142620.16974964X-RAY DIFFRACTION100
3.39-4.260.1752650.15235028X-RAY DIFFRACTION100
4.27-49.430.18542780.16285273X-RAY DIFFRACTION100

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