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- PDB-8y54: Three-dimensional structure of homo-dimer of cystathione beta lya... -

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Basic information

Entry
Database: PDB / ID: 8y54
TitleThree-dimensional structure of homo-dimer of cystathione beta lyase 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
cysteine-S-conjugate beta-lyase
Similarity search - Component
Biological speciesLactobacillus delbrueckii subsp. lactis DSM 20072 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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
DepositionJan 31, 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


Theoretical massNumber of molelcules
Total (without water)88,1162
Polymers88,1162
Non-polymers00
Water6,161342
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-31 kcal/mol
Surface area27930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.470, 91.060, 80.870
Angle α, β, γ (deg.)90.00, 125.27, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-557-

HOH

21A-564-

HOH

31B-482-

HOH

41B-577-

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
Source: (gene. exp.) Lactobacillus delbrueckii subsp. lactis DSM 20072 (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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / Source method: isolated from a natural source / Formula: H2O
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: 1.92 Å3/Da / Density % sol: 35.89 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: Magnesium formate dihydrate, Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: oxford cryosystems 700 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97861 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 1.78→38.95 Å / Num. obs: 63450 / % possible obs: 99.6 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 13.2
Reflection shellResolution: 1.78→1.83 Å / Rmerge(I) obs: 1.17 / Num. unique obs: 4699

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Processing

Software
NameVersionClassification
PHENIXv1.16refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→38.95 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2319 2000 -
Rwork0.2075 --
obs-63450 99.7 %
Refinement stepCycle: LAST / Resolution: 1.78→38.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6148 0 0 342 6490
LS refinement shellResolution: 1.78→1.84 Å
RfactorNum. reflection% reflection
Rfree0.2319 --
Rwork0.2057 --
obs-6129 99.5 %

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