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- PDB-8wko: Crystal structure of O-acetylhomoserine sulfhydrylase from Lactob... -

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Basic information

Entry
Database: PDB / ID: 8wko
TitleCrystal structure of O-acetylhomoserine sulfhydrylase from Lactobacillus plantarum in the closed form
ComponentsL-methionine gamma-lyase
KeywordsLYASE / O-acetylhomoserine sulfhydrylase
Function / homology
Function and homology information


O-acetylhomoserine aminocarboxypropyltransferase / O-acetylhomoserine aminocarboxypropyltransferase activity / cystathionine gamma-synthase / methionine gamma-lyase / methionine gamma-lyase activity / transsulfuration / pyridoxal phosphate binding
Similarity search - Function
O-acetylhomoserine/O-acetylserine sulfhydrylase / Cys/Met metabolism enzymes pyridoxal-phosphate attachment site. / Cys/Met metabolism, pyridoxal phosphate-dependent enzyme / Cys/Met metabolism PLP-dependent enzyme / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Chem-LLP / PROLINE / L-methionine gamma-lyase
Similarity search - Component
Biological speciesLactiplantibacillus plantarum JDM1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsOda, K. / Matoba, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Appl.Environ.Microbiol. / Year: 2024
Title: pH-dependent regulation of an acidophilic O -acetylhomoserine sulfhydrylase from Lactobacillus plantarum.
Authors: Matoba, Y. / Oda, K. / Wataeda, M. / Kanemori, H. / Matsuo, K.
History
DepositionSep 28, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Database references / Category: citation / citation_author
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Revision 1.2Jun 5, 2024Group: Database references / Category: citation / citation_author
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Revision 1.3Jun 19, 2024Group: Database references / Category: citation / citation_author
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-methionine gamma-lyase
B: L-methionine gamma-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,36910
Polymers96,0232
Non-polymers1,3468
Water00
1
A: L-methionine gamma-lyase
B: L-methionine gamma-lyase
hetero molecules

A: L-methionine gamma-lyase
B: L-methionine gamma-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,73820
Polymers192,0464
Non-polymers2,69216
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area23580 Å2
ΔGint-283 kcal/mol
Surface area46570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.822, 155.822, 259.262
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein L-methionine gamma-lyase


Mass: 48011.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactiplantibacillus plantarum JDM1 (bacteria)
Gene: mgl / Plasmid: pET28 / Production host: Escherichia coli B (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): pLysS / References: UniProt: A0A0G9F7S9
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-LLP / (2S)-2-amino-6-[[3-hydroxy-2-methyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]hexanoic acid / N'-PYRIDOXYL-LYSINE-5'-MONOPHOSPHATE


Type: L-peptide linking / Mass: 375.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H22N3O7P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO2
Has ligand of interestY

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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: 3.15 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: potassium sodium tartrate, (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Jul 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→100 Å / Num. obs: 26476 / % possible obs: 99 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.109 / Χ2: 1.008 / Net I/σ(I): 6.2 / Num. measured all: 255330
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.9-36.60.49223750.454190.8
3-3.128.40.46326390.478199.1
3.12-3.2710.10.38826410.5161100
3.27-3.4410.70.29526560.591100
3.44-3.6510.70.226530.7721100
3.65-3.9410.60.13926500.9981100
3.94-4.3310.40.11326771.2991100
4.33-4.9610.20.08826931.5361100
4.96-6.259.90.07926931.4921100
6.25-1008.60.0527991.68199.8

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.91→48.4 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2622 1308 4.95 %
Rwork0.2025 --
obs0.2054 26399 98.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.91→48.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6473 0 33 0 6506
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126653
X-RAY DIFFRACTIONf_angle_d1.8339095
X-RAY DIFFRACTIONf_dihedral_angle_d16.672922
X-RAY DIFFRACTIONf_chiral_restr0.1121062
X-RAY DIFFRACTIONf_plane_restr0.011180
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.91-3.030.36261270.30912468X-RAY DIFFRACTION88
3.03-3.160.331450.28682778X-RAY DIFFRACTION99
3.16-3.330.34481520.26592776X-RAY DIFFRACTION100
3.33-3.540.26791540.2392800X-RAY DIFFRACTION100
3.54-3.810.26151470.21292805X-RAY DIFFRACTION100
3.81-4.20.28781540.19282823X-RAY DIFFRACTION100
4.2-4.80.23011340.1782844X-RAY DIFFRACTION100
4.8-6.050.23891340.18452874X-RAY DIFFRACTION100
6.05-48.40.23231610.17332923X-RAY DIFFRACTION99

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