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

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Basic information

Entry
Database: PDB / ID: 9kau
TitleThree-dimensional structure of homo-dimer of cystathione beta lyase/PLP/+L-alliin complex from Bacillus cereus(BcPatB)
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 / biosynthetic process / catalytic activity / pyridoxal phosphate binding
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 speciesBacillus cereus ATCC 14579 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 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: Homodimer of cystatohinine beta lyase PatB/PLP/L-(+)-alliin complex from Bacillus cereus(NCBI Reference Sequence: WP_001974105.1)
Authors: Liu, Y. / Yang, C.
History
DepositionOct 29, 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)88,9613
Polymers88,7842
Non-polymers1771
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-34 kcal/mol
Surface area28820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.223, 85.522, 168.077
Angle α, β, γ (deg.)90.00, 91.12, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 44391.781 Da / Num. of mol.: 2
Mutation: E51K, L179I, Q180K, E286K, Q296K, I302M, T304D, A308T, R326A, K328N, N332D, A336K
Source method: isolated from a genetically manipulated source
Details: Homodimer of cystatohinine beta lyase PatB/PLP/L-(+)-alliin complex from Bacillus cereus(NCBI Reference Sequence: WP_001974105.1)
Source: (gene. exp.) Bacillus cereus ATCC 14579 (bacteria) / Strain: ATCC 14579 / Gene: BK746_00885 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A9X6FDP0, 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.: 98 / 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

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: 0.997 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 25, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.997 Å / Relative weight: 1
ReflectionResolution: 1.88→168.05 Å / Num. obs: 119803 / % possible obs: 97.7 % / Redundancy: 5.4 % / Rpim(I) all: 0.145 / Net I/σ(I): 5
Reflection shellResolution: 1.88→1.98 Å / Rmerge(I) obs: 1.415 / Num. unique obs: 15330

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Processing

Software
NameVersionClassification
PHENIX1.16refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→35.46 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.3931 1993 -
Rwork0.3594 --
obs-119563 99.8 %
Refinement stepCycle: LAST / Resolution: 1.88→35.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6078 0 41 98 6217
LS refinement shellResolution: 1.88→1.95 Å
RfactorNum. reflection% reflection
Rfree0.3931 --
Rwork0.3594 4871 -
obs--95.6 %

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