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- PDB-8y7s: Crystal structure of a benzaldehyde lyase mutant M6 from Herbicon... -

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Basic information

Entry
Database: PDB / ID: 8y7s
TitleCrystal structure of a benzaldehyde lyase mutant M6 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
THIAMINE DIPHOSPHATE / Thiamine pyrophosphate-binding protein
Similarity search - Component
Biological speciesHerbiconiux sp. SALV-R1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 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 5, 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

Downloads & links

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Assembly

Deposited unit
A: Thiamine pyrophosphate-binding protein
B: Thiamine pyrophosphate-binding protein
C: Thiamine pyrophosphate-binding protein
D: Thiamine pyrophosphate-binding protein
E: Thiamine pyrophosphate-binding protein
F: Thiamine pyrophosphate-binding protein
G: Thiamine pyrophosphate-binding protein
H: Thiamine pyrophosphate-binding protein
I: Thiamine pyrophosphate-binding protein
J: Thiamine pyrophosphate-binding protein
K: Thiamine pyrophosphate-binding protein
L: Thiamine pyrophosphate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)705,93136
Polymers700,53512
Non-polymers5,39524
Water14,196788
1
A: Thiamine pyrophosphate-binding protein
B: Thiamine pyrophosphate-binding protein
E: Thiamine pyrophosphate-binding protein
F: Thiamine pyrophosphate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,31012
Polymers233,5124
Non-polymers1,7988
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24930 Å2
ΔGint-130 kcal/mol
Surface area61160 Å2
MethodPISA
2
C: Thiamine pyrophosphate-binding protein
D: Thiamine pyrophosphate-binding protein
hetero molecules

H: Thiamine pyrophosphate-binding protein
K: Thiamine pyrophosphate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,31012
Polymers233,5124
Non-polymers1,7988
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area24880 Å2
ΔGint-133 kcal/mol
Surface area60680 Å2
MethodPISA
3
J: Thiamine pyrophosphate-binding protein
L: Thiamine pyrophosphate-binding protein
hetero molecules

G: Thiamine pyrophosphate-binding protein
hetero molecules

I: Thiamine pyrophosphate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,31012
Polymers233,5124
Non-polymers1,7988
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445-x-1/2,y-1/2,-z1
crystal symmetry operation4_455-x-1/2,y+1/2,-z1
Buried area24560 Å2
ΔGint-135 kcal/mol
Surface area61120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)333.789, 98.696, 231.654
Angle α, β, γ (deg.)90.00, 108.05, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Thiamine pyrophosphate-binding protein


Mass: 58377.934 Da / Num. of mol.: 12 / Mutation: A27I, V29I, G417S,E549L, I552L, M533L
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
#2: Chemical
ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C12H19N4O7P2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 788 / 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: 2.58 Å3/Da / Density % sol: 52.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 25% PEG 4000, 40% 1,2,6-Hexanetriol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.68→50 Å / Num. obs: 201314 / % possible obs: 99.8 % / Redundancy: 10.5 % / CC1/2: 0.981 / CC star: 0.995 / Rmerge(I) obs: 0.307 / Rpim(I) all: 0.097 / Rrim(I) all: 0.322 / Χ2: 0.559 / Net I/σ(I): 2.2 / Num. measured all: 2121106
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.68-2.787.81.361196900.7010.9080.4681.4440.41898.7
2.78-2.899.61.157200630.8220.950.3731.2180.42799.8
2.89-3.0210.40.984200030.8670.9640.3111.0330.4399.9
3.02-3.1811.10.781201090.920.9790.2410.8190.445100
3.18-3.3810.80.57200480.9490.9870.1790.5990.468100
3.38-3.6410.90.37201610.9730.9930.1160.3880.511100
3.64-411.40.254201470.9870.9970.0780.2660.566100
4-4.5811.20.169201970.9920.9980.0520.1770.674100
4.58-5.7711.40.138202770.9940.9990.0430.1450.718100
5.77-5010.70.096206190.9970.9990.030.1010.85100

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.68→29.19 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2357 9996 5 %
Rwork0.1887 --
obs0.191 199971 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.68→29.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms48846 0 0 788 49634
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00749862
X-RAY DIFFRACTIONf_angle_d1.18868217
X-RAY DIFFRACTIONf_dihedral_angle_d9.5067448
X-RAY DIFFRACTIONf_chiral_restr0.0958147
X-RAY DIFFRACTIONf_plane_restr0.0218980
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.68-2.770.34519660.295318342X-RAY DIFFRACTION97
2.77-2.880.30829940.2518904X-RAY DIFFRACTION99
2.88-3.010.30249980.237618969X-RAY DIFFRACTION99
3.01-3.170.299410020.233619019X-RAY DIFFRACTION99
3.17-3.370.262510000.213819023X-RAY DIFFRACTION100
3.37-3.630.254810060.194819091X-RAY DIFFRACTION100
3.63-40.223710020.17619075X-RAY DIFFRACTION100
4-4.570.193710070.155619169X-RAY DIFFRACTION100
4.57-5.750.190210120.149619218X-RAY DIFFRACTION100
5.75-29.190.185310090.154419165X-RAY DIFFRACTION98

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