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- PDB-9m0q: The Structural Complex of Inactivated Lactobacillus delbrueckii C... -

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Basic information

Entry
Database: PDB / ID: 9m0q
TitleThe Structural Complex of Inactivated Lactobacillus delbrueckii Cystathionine beta-Lyase Mutant (LdPatB A34D) with Its Substrate L-(+)-Alliin
Componentscysteine-S-conjugate beta-lyase
KeywordsBIOSYNTHETIC PROTEIN / C-S cleavage reaction / L-cysteine-S-conjugate
Function / homology
Function and homology information


cysteine-S-conjugate beta-lyase / transaminase activity / biosynthetic process / pyridoxal phosphate binding / lyase activity
Similarity search - Function
: / Putative C-S lyase / Aminotransferase, class I/classII / Aminotransferase class I and II / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
: / cysteine-S-conjugate beta-lyase
Similarity search - Component
Biological speciesLactobacillus delbrueckii subsp. lactis DSM 20072 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsLiu, Y. / Yang, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)Project no. 42077214 China
CitationJournal: To Be Published
Title: The Structural Complex of Inactivated Lactobacillus delbrueckii Cystathionine beta-Lyase Mutant (LdPatB A34D) with Its Substrate L-(+)-Alliin
Authors: Liu, Y. / Yang, C.
History
DepositionFeb 25, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cysteine-S-conjugate beta-lyase
B: cysteine-S-conjugate beta-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,8383
Polymers88,6612
Non-polymers1771
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-29 kcal/mol
Surface area27720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.831, 91.682, 80.871
Angle α, β, γ (deg.)90.00, 125.06, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-812-

HOH

21B-545-

HOH

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Components

#1: Protein cysteine-S-conjugate beta-lyase


Mass: 44330.301 Da / Num. of mol.: 2 / Mutation: A34D/V311E/N326D
Source method: isolated from a genetically manipulated source
Details: NCBI Reference Sequence: WP_236160334.1
Source: (gene. exp.) Lactobacillus delbrueckii subsp. lactis DSM 20072 (bacteria)
Gene: LDL72_07215 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0AAC9VP02, cysteine-S-conjugate beta-lyase
#2: Chemical ChemComp-OO0 / ALLIIN / 2-azanyl-3-prop-2-enylsulfinyl-propanoic acid


Mass: 177.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11NO3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 1.92 Å3/Da / Density % sol: 36.06 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Magnesium formate dihydrate (15-25 % w/v) Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97907 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 29, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 2.18→64.78 Å / Num. obs: 34610 / % possible obs: 99.6 % / Redundancy: 5.6 % / Rpim(I) all: 0.103 / Net I/σ(I): 3.6
Reflection shellResolution: 2.18→2.3 Å / Num. unique obs: 4969 / Rpim(I) all: 0.942

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Processing

Software
NameVersionClassification
PHENIXv1.16refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.18→45.77 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.3032 2000 -
Rwork0.251 --
obs-34590 99.7 %
Refinement stepCycle: LAST / Resolution: 2.18→45.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6096 0 11 93 6200
LS refinement shellResolution: 2.18→2.26 Å
RfactorNum. reflection% reflection
Rfree0.3 --
Rwork0.25 3345 -
obs--98.1 %

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