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- PDB-6s0c: Crystal structure of methionine gamma-lyase from Citrobacter freu... -

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Basic information

Entry
Database: PDB / ID: 6s0c
TitleCrystal structure of methionine gamma-lyase from Citrobacter freundii modified by dimethylthiosulfinate
ComponentsCystathionine gamma-synthase
KeywordsLYASE / METHIONINE GAMMA-LYASE
Function / homology
Function and homology information


methionine gamma-lyase / methionine gamma-lyase activity / transsulfuration / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
L-methionine gamma-lyase / 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
TRIETHYLENE GLYCOL / PYRIDOXAL-5'-PHOSPHATE / L-methionine gamma-lyase
Similarity search - Component
Biological speciesCitrobacter freundii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsRevtovich, S.V. / Morozova, E.A. / Nikulin, A.D. / Demidkina, T.V.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation15-14-00009 Russian Federation
CitationJournal: Biochimie / Year: 2020
Title: Sulfoxides of sulfur-containing amino acids are suicide substrates of Citrobacter freundii methionine gamma-lyase. Structural bases of the enzyme inactivation.
Authors: Revtovich, S. / Morozova, E. / Kulikova, V. / Koval, V. / Anufrieva, N. / Nikulin, A. / Demidkina, T.
History
DepositionJun 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cystathionine gamma-synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4723
Polymers43,0751
Non-polymers3972
Water6,089338
1
A: Cystathionine gamma-synthase
hetero molecules

A: Cystathionine gamma-synthase
hetero molecules

A: Cystathionine gamma-synthase
hetero molecules

A: Cystathionine gamma-synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,89012
Polymers172,3004
Non-polymers1,5898
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area24270 Å2
ΔGint-109 kcal/mol
Surface area45440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.784, 123.255, 128.328
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-511-

HOH

21A-662-

HOH

31A-725-

HOH

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Components

#1: Protein Cystathionine gamma-synthase / Methionine gamma-lyase


Mass: 43075.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrobacter freundii (bacteria)
Gene: mdeA, megL, AM363_27345, AN672_11005, AZ002_001464, BED45_02240, CES93_01075, CFA70_17460, EOL10_00980, HMPREF3212_02785, NCTC13639_00292, TO64_18625
Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0A0A5P8W7, methionine gamma-lyase
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / Source method: isolated from a natural source / Formula: H2O
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: 2.59 Å3/Da / Density % sol: 52.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 50 mM Tris-HCl, pH 8.5, 0.5 mM PLP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.46→50 Å / Num. obs: 76641 / % possible obs: 97.8 % / Redundancy: 4.45 % / CC1/2: 1 / Rrim(I) all: 0.054 / Net I/σ(I): 20.48
Reflection shellResolution: 1.46→1.55 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 2.22 / Num. unique obs: 120129 / CC1/2: 0.75 / Rrim(I) all: 0.701 / % possible all: 70.5

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RFV

2rfv


Resolution: 1.46→40.411 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.97
RfactorNum. reflection% reflection
Rfree0.1724 2099 2.74 %
Rwork0.1374 --
obs0.1384 76627 97.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.46→40.411 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2974 0 10 338 3322
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053176
X-RAY DIFFRACTIONf_angle_d0.8794329
X-RAY DIFFRACTIONf_dihedral_angle_d8.2421813
X-RAY DIFFRACTIONf_chiral_restr0.081498
X-RAY DIFFRACTIONf_plane_restr0.005563
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4596-1.49350.2721340.234763X-RAY DIFFRACTION95
1.4935-1.53090.25671360.21154871X-RAY DIFFRACTION97
1.5309-1.57220.22841360.19284817X-RAY DIFFRACTION96
1.5722-1.61850.24531380.17964907X-RAY DIFFRACTION97
1.6185-1.67080.22571390.17044915X-RAY DIFFRACTION97
1.6708-1.73050.21481380.15674917X-RAY DIFFRACTION97
1.7305-1.79980.21941390.14234942X-RAY DIFFRACTION98
1.7998-1.88170.17591390.13564927X-RAY DIFFRACTION98
1.8817-1.98090.18021400.13434975X-RAY DIFFRACTION98
1.9809-2.1050.15931410.124994X-RAY DIFFRACTION99
2.105-2.26750.15911420.12285035X-RAY DIFFRACTION99
2.2675-2.49560.17341410.12915012X-RAY DIFFRACTION99
2.4956-2.85670.16671430.13215079X-RAY DIFFRACTION99
2.8567-3.59880.15071440.13215122X-RAY DIFFRACTION99
3.5988-40.4270.15211490.12935252X-RAY DIFFRACTION98

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