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- PDB-5dx5: Crystal structure of methionine gamma-lyase from Clostridium spor... -

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Basic information

Entry
Database: PDB / ID: 5dx5
TitleCrystal structure of methionine gamma-lyase from Clostridium sporogenes
ComponentsMethionine gamma-lyase
KeywordsLYASE / methionine gamma-lyase / Clostridium sporogenes
Function / homology
Function and homology information


methionine gamma-lyase / methionine gamma-lyase activity / transsulfuration / pyridoxal phosphate binding
Similarity search - Function
L-methionine gamma-lyase / Cys/Met metabolism enzymes pyridoxal-phosphate attachment site. / Cys/Met metabolism, pyridoxal phosphate-dependent enzyme / Cys/Met metabolism PLP-dependent enzyme / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain ...L-methionine gamma-lyase / Cys/Met metabolism enzymes pyridoxal-phosphate attachment site. / Cys/Met metabolism, pyridoxal phosphate-dependent enzyme / Cys/Met metabolism PLP-dependent enzyme / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / L-methionine gamma-lyase
Similarity search - Component
Biological speciesClostridium sporogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsRevtovich, S.V. / Nikulin, A.D. / Morozova, E.A. / Anufrieva, N.V. / Demidkina, T.V.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Scientific Foundation15-14-00009 Russian Federation
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2016
Title: Structure of methionine gamma-lyase from Clostridium sporogenes.
Authors: Revtovich, S. / Anufrieva, N. / Morozova, E. / Kulikova, V. / Nikulin, A. / Demidkina, T.
History
DepositionSep 23, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2016Group: Database references
Revision 1.2Jan 10, 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: Methionine gamma-lyase
B: Methionine gamma-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,7487
Polymers87,1592
Non-polymers5885
Water3,495194
1
A: Methionine gamma-lyase
B: Methionine gamma-lyase
hetero molecules

A: Methionine gamma-lyase
B: Methionine gamma-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,49514
Polymers174,3194
Non-polymers1,17610
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area24030 Å2
ΔGint-214 kcal/mol
Surface area46860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.090, 91.090, 175.929
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-674-

HOH

21B-690-

HOH

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Components

#1: Protein Methionine gamma-lyase


Mass: 43579.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium sporogenes (bacteria) / Gene: megL, CLOSPO_00030 / Production host: Escherichia coli (E. coli) / References: UniProt: J7TA22, methionine gamma-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
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: MGL 20mg/ml, PEG MME 2000 35%, 50 ml TrisHCl (pH=8.5), 0.2 mM PLP

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Data collection

DiffractionMean temperature: 100 K
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: 2.37→50 Å / Num. all: 57232 / Num. obs: 57232 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rmerge(I) obs: 0.097 / Rsym value: 0.088 / Net I/σ(I): 17
Reflection shellResolution: 2.37→2.45 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.9 / % possible all: 100

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Processing

Software
NameVersionClassification
MxCuBEdata collection
XDSdata reduction
SCALAdata scaling
PHASERphasing
PHENIX1.10_2155refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RFV

2rfv


Resolution: 2.37→50 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.25 / Phase error: 21.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2249 2075 3.63 %Random selection
Rwork0.1624 ---
obs0.1646 57225 99.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.37→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6092 0 33 194 6319
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086236
X-RAY DIFFRACTIONf_angle_d1.0278431
X-RAY DIFFRACTIONf_dihedral_angle_d14.3613724
X-RAY DIFFRACTIONf_chiral_restr0.057957
X-RAY DIFFRACTIONf_plane_restr0.0051082
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3689-2.4240.28161390.2373678X-RAY DIFFRACTION99
2.424-2.48460.2931340.22433697X-RAY DIFFRACTION100
2.4846-2.55170.27211390.21073638X-RAY DIFFRACTION100
2.5517-2.62680.30761390.2093706X-RAY DIFFRACTION100
2.6268-2.71160.27631380.20183681X-RAY DIFFRACTION99
2.7116-2.80850.30151360.20413650X-RAY DIFFRACTION99
2.8085-2.92090.21831380.17853689X-RAY DIFFRACTION100
2.9209-3.05380.24311430.17113704X-RAY DIFFRACTION100
3.0538-3.21480.1991420.16833670X-RAY DIFFRACTION100
3.2148-3.41620.231450.15733678X-RAY DIFFRACTION100
3.4162-3.67980.20591380.14473650X-RAY DIFFRACTION99
3.6798-4.04990.19051370.13443701X-RAY DIFFRACTION100
4.0499-4.63550.17741350.12263689X-RAY DIFFRACTION100
4.6355-5.83830.21161410.14643655X-RAY DIFFRACTION99
5.8383-45.55340.22191310.15833664X-RAY DIFFRACTION99

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