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- PDB-5d5s: Crystal structure of methionine gamma-lyase from Citrobacter freu... -

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Basic information

Entry
Database: PDB / ID: 5d5s
TitleCrystal structure of methionine gamma-lyase from Citrobacter freundii, S339A mutant
ComponentsMethionine gamma-lyase
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 / 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 ...L-methionine gamma-lyase / 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
DI(HYDROXYETHYL)ETHER / PYRIDOXAL-5'-PHOSPHATE / L-methionine gamma-lyase
Similarity search - Component
Biological speciesCitrobacter freundii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsRevtovich, S.V. / Nikulin, A.D. / Anufrieva, N.V. / Morozova, E.A. / Demidkina, T.V.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
RFBR Russian Federation
CitationJournal: To Be Published
Title: The crystal structure of methionine gamma-lyase from Citrobacter freundii, S339A mutant
Authors: Revtovich, S.V. / Nikulin, A.D. / Anufrieva, N.V. / Morozova, E.A. / Demidkina, T.V.
History
DepositionAug 11, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 2.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methionine gamma-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3454
Polymers42,9691
Non-polymers3763
Water7,080393
1
A: Methionine gamma-lyase
hetero molecules

A: Methionine gamma-lyase
hetero molecules

A: Methionine gamma-lyase
hetero molecules

A: Methionine gamma-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,38016
Polymers171,8754
Non-polymers1,50512
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area22520 Å2
ΔGint-142 kcal/mol
Surface area47340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.659, 123.090, 128.785
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-504-

HOH

21A-516-

HOH

31A-702-

HOH

41A-729-

HOH

51A-827-

HOH

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Components

#1: Protein Methionine gamma-lyase


Mass: 42968.801 Da / Num. of mol.: 1 / Mutation: S339A
Source method: isolated from a genetically manipulated source
Details: S339A substitution and some Cys were oxidized to CSO
Source: (gene. exp.) Citrobacter freundii (bacteria) / Gene: TN42_08855, TO64_18625 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0A5P8W7, methionine gamma-lyase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


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


Mass: 18.015 Da / Num. of mol.: 393 / 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: 2.6 Å3/Da / Density % sol: 52.67 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 5% PEG2000 MME, 50 MM TRIS-HCL, 0.2 MM PLP, 0.25% DTT, PH 8.5,

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 7, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 49574 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 23.5
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 4.7 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MxCuBEdata collection
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RFV

2rfv


Resolution: 1.7→30 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2051 2503 5.08 %random
Rwork0.173 ---
obs0.1745 49320 98.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2879 0 8 393 3280
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072981
X-RAY DIFFRACTIONf_angle_d1.0954052
X-RAY DIFFRACTIONf_dihedral_angle_d15.9121096
X-RAY DIFFRACTIONf_chiral_restr0.047469
X-RAY DIFFRACTIONf_plane_restr0.005527
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.73270.3141260.23362555X-RAY DIFFRACTION97
1.7327-1.76810.26511310.22222483X-RAY DIFFRACTION97
1.7681-1.80650.24761390.2222558X-RAY DIFFRACTION98
1.8065-1.84850.2841650.20772507X-RAY DIFFRACTION98
1.8485-1.89470.26441340.21822617X-RAY DIFFRACTION100
1.8947-1.9460.25391600.20582587X-RAY DIFFRACTION100
1.946-2.00320.23661540.19282533X-RAY DIFFRACTION100
2.0032-2.06780.22141250.18322636X-RAY DIFFRACTION100
2.0678-2.14170.19091410.18372592X-RAY DIFFRACTION100
2.1417-2.22740.24151490.18522619X-RAY DIFFRACTION99
2.2274-2.32880.21541310.17922587X-RAY DIFFRACTION99
2.3288-2.45150.21121360.17342606X-RAY DIFFRACTION99
2.4515-2.6050.2221410.1752604X-RAY DIFFRACTION99
2.605-2.80590.20821320.17182608X-RAY DIFFRACTION99
2.8059-3.0880.20861350.17232621X-RAY DIFFRACTION99
3.088-3.53410.18981300.162651X-RAY DIFFRACTION99
3.5341-4.44980.16441360.14542689X-RAY DIFFRACTION99
4.4498-300.17271380.16282764X-RAY DIFFRACTION98

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