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

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Basic information

Entry
Database: PDB / ID: 9jva
TitleThree-dimensional structure of homo-dimer of cystathione beta lyase/PLP 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 subsp. lactis DSM 20072 (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)/PLP complex of Lactobacillus lactobacillus delbrueckii at 1.53 ANG
Authors: Liu, Y. / Yang, C.
History
DepositionOct 8, 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)88,6114
Polymers88,1162
Non-polymers4942
Water12,016667
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-36 kcal/mol
Surface area28800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.661, 94.218, 84.762
Angle α, β, γ (deg.)90.00, 126.97, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-541-

HOH

21A-789-

HOH

31A-790-

HOH

41B-747-

HOH

51B-777-

HOH

61B-784-

HOH

71B-788-

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: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 667 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.09 Å3/Da / Density % sol: 41.25 %
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: 0.97 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: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.56→66 Å / Num. obs: 65530 / % possible obs: 99.6 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 10
Reflection shellResolution: 1.56→1.64 Å / Rmerge(I) obs: 0.534 / Num. unique obs: 1348

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Processing

Software
NameVersionClassification
PHENIX1.16-3549-000refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.08→33.86 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.1945 2000 -
Rwork0.1661 --
obs-65530 98.7 %
Refinement stepCycle: LAST / Resolution: 2.08→33.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6156 0 32 667 6855
LS refinement shellResolution: 2.08→2.28 Å
RfactorNum. reflection% reflection
Rfree0.1945 --
Rwork0.1661 --
obs-10189 96.6 %

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