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- PDB-9uuw: Crystal structure of Yarrowia lipolytica methionine gamma-lyase i... -

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Basic information

Entry
Database: PDB / ID: 9uuw
TitleCrystal structure of Yarrowia lipolytica methionine gamma-lyase in complex with L-methionine
ComponentsCys/Met metabolism PLP-dependent enzyme-domain-containing protein
KeywordsLYASE / PLP / Methionine
Function / homology
Function and homology information


carbon-sulfur lyase activity / transsulfuration / pyridoxal phosphate binding / nucleus / cytoplasm
Similarity search - Function
: / 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
METHIONINE / Cys/Met metabolism PLP-dependent enzyme-domain-containing protein
Similarity search - Component
Biological speciesYarrowia lipolytica (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.04 Å
AuthorsChen, X. / Shi, M.W. / Yan, C. / Zhu, L.W. / Jia, K.Z.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFC2106100 China
CitationJournal: To Be Published
Title: Crystal structure of Yarrowia lipolytica methionine gamma-lyase in complex with L-methionine
Authors: Chen, X. / Shi, M.W. / Yan, C. / Zhu, L.W. / Jia, K.Z.
History
DepositionMay 8, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 13, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cys/Met metabolism PLP-dependent enzyme-domain-containing protein
B: Cys/Met metabolism PLP-dependent enzyme-domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,7054
Polymers84,4062
Non-polymers2982
Water00
1
A: Cys/Met metabolism PLP-dependent enzyme-domain-containing protein
B: Cys/Met metabolism PLP-dependent enzyme-domain-containing protein
hetero molecules

A: Cys/Met metabolism PLP-dependent enzyme-domain-containing protein
B: Cys/Met metabolism PLP-dependent enzyme-domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,4108
Polymers168,8134
Non-polymers5974
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area18740 Å2
ΔGint-100 kcal/mol
Surface area45970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.054, 166.054, 81.314
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Cys/Met metabolism PLP-dependent enzyme-domain-containing protein / methionine gamma-lyase


Mass: 42203.238 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: B0I71DRAFT_129673, YALI1_C30440g / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1D8NC95
#2: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO2S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: 3.83 Å3/Da / Density % sol: 67.92 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion / Details: 0.2M NaCl, 0.1M CAPS, pH 10.3, 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Sep 17, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.04→70.782 Å / Num. obs: 25137 / % possible obs: 100 % / Redundancy: 1.9 % / CC1/2: 0.954 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.136 / Rrim(I) all: 0.192 / Net I/σ(I): 6.6
Reflection shellResolution: 3.04→3.25 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.241 / Mean I/σ(I) obs: 2 / Num. unique obs: 4518 / CC1/2: 0.582 / Rpim(I) all: 0.241 / Rrim(I) all: 0.341 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.04→70.782 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2662 1210 4.85 %
Rwork0.2327 --
obs0.2344 24959 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.04→70.782 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5595 0 18 0 5613
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035741
X-RAY DIFFRACTIONf_angle_d0.6797796
X-RAY DIFFRACTIONf_dihedral_angle_d16.3152046
X-RAY DIFFRACTIONf_chiral_restr0.047876
X-RAY DIFFRACTIONf_plane_restr0.0041006
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0403-3.1620.33811430.30942596X-RAY DIFFRACTION100
3.162-3.30590.35671190.29022663X-RAY DIFFRACTION100
3.3059-3.48020.35981100.28152646X-RAY DIFFRACTION100
3.4802-3.69820.33051280.27842609X-RAY DIFFRACTION98
3.6982-3.98380.24131340.24132574X-RAY DIFFRACTION98
3.9838-4.38460.25181550.21442613X-RAY DIFFRACTION99
4.3846-5.01890.21161460.1842638X-RAY DIFFRACTION100
5.0189-6.32270.25191350.21692668X-RAY DIFFRACTION100
6.3227-70.7820.20931400.18132742X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 57.1596 Å / Origin y: -63.1034 Å / Origin z: 25.3619 Å
111213212223313233
T0.3052 Å20.0088 Å20.023 Å2-0.3023 Å2-0.045 Å2--0.1124 Å2
L1.2483 °20.4247 °20.2405 °2-0.593 °20.0718 °2--1.5751 °2
S0.0515 Å °-0.067 Å °-0.0944 Å °0.039 Å °-0.0131 Å °-0.1173 Å °-0.0563 Å °0.027 Å °-0.0501 Å °
Refinement TLS groupSelection details: all

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