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- PDB-9k71: Three-dimensional structure of homo-dimer of cystathione beta lya... -

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Basic information

Entry
Database: PDB / ID: 9k71
TitleThree-dimensional structure of homo-dimer of cystathione beta lyase/PLP 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 activity / cysteine-S-conjugate beta-lyase / L-aspartate:2-oxoglutarate aminotransferase 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: 2.28 Å
AuthorsLiu, Y. / Yang, C.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)Project no. 42077214 China
Other government2021CXGC010803 China
CitationJournal: To Be Published
Title: Homodimer of cystatohinine beta lyase PatB/PLP complex from Bacillus cereus
Authors: Liu, Y. / Yang, C.
History
DepositionOct 23, 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)88,7842
Polymers88,7842
Non-polymers00
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6040 Å2
ΔGint-37 kcal/mol
Surface area28940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.421, 84.652, 163.376
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 44391.781 Da / Num. of mol.: 2
Mutation: E51K; N66D; Y131C; Q147K; L179I; Q180K; A220E; Q251H; S255A; E286K; Q296K ; W299C; I302M; T304D; A308T; R326A;K328N; N332D; A336K
Source method: isolated from a genetically manipulated source
Details: Homodimer of cystatohinine beta lyase PatB/PLP complex from Bacillus cereus (NCBI Reference Sequence: WP_001974105.1)
Source: (gene. exp.) Bacillus cereus ATCC 14579 (bacteria) / Strain: ATCC 14579 / Gene: BC_4906 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q816F3, cysteine-S-conjugate beta-lyase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.09 Å3/Da / Density % sol: 41.18 %
Crystal growTemperature: 289.15 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: 0.99 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.28→42.33 Å / Num. obs: 34049 / % possible obs: 98.3 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 10.7
Reflection shellResolution: 2.28→2.4 Å / Rmerge(I) obs: 0.904 / Num. unique obs: 4764

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Processing

Software
NameVersionClassification
PHENIX1.16refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→42.33 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.3097 1999 -
Rwork0.2291 --
obs-33844 99.4 %
Refinement stepCycle: LAST / Resolution: 2.28→42.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6207 0 30 106 6343
LS refinement shellResolution: 2.28→2.3609 Å
RfactorNum. reflection% reflection
Rfree0.3097 --
Rwork0.2291 2799 -
obs--94.9 %

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