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- PDB-2rfv: High resolution structure of L-methionine gamma-lyase from Citrob... -

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Basic information

Entry
Database: PDB / ID: 2rfv
TitleHigh resolution structure of L-methionine gamma-lyase from Citrobacter freundii
ComponentsMethionine gamma-lyase
KeywordsLYASE / PYRIDOXAL-5'-PHOSPHATE / PLP-DEPENDENT ENZYME
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
L-methionine gamma-lyase
Similarity search - Component
Biological speciesCitrobacter freundii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.355 Å
AuthorsNikulin, A.D. / Revtovich, S.V. / Morozova, E.A. / Nevskaya, N.A. / Nikonov, S.V. / Garber, M.B. / Demidkina, T.V.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: High-resolution structure of methionine gamma-lyase from Citrobacter freundii.
Authors: Nikulin, A. / Revtovich, S. / Morozova, E. / Nevskaya, N. / Nikonov, S. / Garber, M. / Demidkina, T.
History
DepositionOct 2, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)43,2862
Polymers43,2511
Non-polymers351
Water6,882382
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)173,1468
Polymers173,0044
Non-polymers1424
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 area20310 Å2
ΔGint-112.6 kcal/mol
Surface area45850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.450, 122.800, 127.920
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-399-

CL

21A-610-

HOH

DetailsThe biological assembly is a tetramer generated from the monomer in the asymmetric unit by the crystallographic symmetry operation.

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Components

#1: Protein Methionine gamma-lyase


Mass: 43251.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrobacter freundii (bacteria) / Gene: megL / Plasmid: PET-MGL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q84AR1, methionine gamma-lyase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THERE IS AN ERROR IN THE DATABASE SEQUENCE.

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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: 2.56 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 35% MMEPEG 2000, 50MM TRIS-HCL,0.2MM PLP, 0.25% DTT, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.843 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.843 Å / Relative weight: 1
ReflectionResolution: 1.35→30 Å / Num. all: 95252 / Num. obs: 95252 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 20.15
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.54 / Num. unique all: 8416 / % possible all: 84.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
MAR345data collection
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y4I

1y4i


Resolution: 1.355→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
Details: In the refinement FLAT BULK SOLVENT MODEL was used.
RfactorNum. reflection% reflectionSelection details
Rfree0.1772 4775 5.01 %random
Rwork0.1515 ---
all0.1528 95252 --
obs-95252 --
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.0222 Å2-6.9534 Å20.9311 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.355→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3169 0 1 382 3552
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_deg1.021
X-RAY DIFFRACTIONf_chiral_restr0.07
X-RAY DIFFRACTIONf_planar_dist0.006
X-RAY DIFFRACTIONf_dihedral_d16.17
LS refinement shellResolution: 1.355→1.37 Å
RfactorNum. reflection% reflection
Rfree0.319 167 -
Rwork0.341 --
obs-2847 98.95 %

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