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- PDB-9jwc: Three-dimensional structure of homo-dimer of cystathione beta lya... -

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Basic information

Entry
Database: PDB / ID: 9jwc
TitleThree-dimensional structure of homo-dimer of cystathione beta lyase/PLP/+L-alliin complex from lactobacillus delbrueckii(LdPatB)
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
: / PYRIDOXAL-5'-PHOSPHATE / cysteine-S-conjugate beta-lyase
Similarity search - Component
Biological speciesLactobacillus delbrueckii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 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: Cystathionine beta-lyase(PatB)of Lactobacillus lactobacillus delbrueckii at 1.78 ?
Authors: Liu, Y. / Yang, C.
History
DepositionOct 10, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 20, 2024Provider: 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)88,7885
Polymers88,1162
Non-polymers6723
Water8,809489
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-36 kcal/mol
Surface area27930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.102, 92.000, 81.586
Angle α, β, γ (deg.)90.00, 126.05, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-734-

HOH

21A-746-

HOH

31B-710-

HOH

41B-721-

HOH

51B-741-

HOH

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Components

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


Mass: 44058.172 Da / Num. of mol.: 2 / Mutation: V311E, N326D
Source method: isolated from a genetically manipulated source
Details: NCBI Reference Sequence: WP_236160334.1 / Source: (gene. exp.) Lactobacillus delbrueckii (bacteria) / Gene: LDL72_07215 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
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: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 489 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 1.98 Å3/Da / Density % sol: 37.93 %
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: 1.75→65.42 Å / Num. obs: 60295 / % possible obs: 87.6 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 16.5
Reflection shellResolution: 1.75→1.85 Å / Rmerge(I) obs: 0.368 / Num. unique obs: 4948

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Processing

Software
NameVersionClassification
PHENIX1.16refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.08→65.42 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2179 2000 -
Rwork0.1872 --
obs-60295 99.6 %
Refinement stepCycle: LAST / Resolution: 2.08→65.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6169 0 43 489 6701
LS refinement shellResolution: 2.08→2.21 Å
RfactorNum. reflection% reflection
Rfree0.2179 --
Rwork0.1872 --
obs-6628 100 %

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