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- PDB-5x2w: Crystal structure of Pseudomonas putida methionine gamma-lyase wi... -

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Basic information

Entry
Database: PDB / ID: 5x2w
TitleCrystal structure of Pseudomonas putida methionine gamma-lyase wild type with L-methionine intermediates
ComponentsL-methionine gamma-lyase
KeywordsLYASE / Pyridoxal 5'-phosphate
Function / homology
Function and homology information


homocysteine desulfhydrase activity / homocysteine desulfhydrase / methionine gamma-lyase / methionine gamma-lyase activity / transsulfuration / pyridoxal phosphate binding / cytoplasm
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 ...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
Chem-3LM / L-methionine gamma-lyase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsShiba, T. / Sato, D. / Harada, S.
CitationJournal: Protein Sci. / Year: 2017
Title: Structural and mechanistic insights into homocysteine degradation by a mutant of methionine gamma-lyase based on substrate-assisted catalysis
Authors: Sato, D. / Shiba, T. / Yunoto, S. / Furutani, K. / Fukumoto, M. / Kudou, D. / Tamura, T. / Inagaki, K. / Harada, S.
History
DepositionFeb 2, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Nov 22, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: L-methionine gamma-lyase
B: L-methionine gamma-lyase
C: L-methionine gamma-lyase
D: L-methionine gamma-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,2088
Polymers170,6944
Non-polymers1,5134
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19400 Å2
ΔGint-94 kcal/mol
Surface area46740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.635, 152.311, 80.487
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
L-methionine gamma-lyase / MGL / Homocysteine desulfhydrase / L-methioninase


Mass: 42673.617 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: mdeA / Production host: Escherichia coli (E. coli)
References: UniProt: P13254, methionine gamma-lyase, homocysteine desulfhydrase
#2: Chemical
ChemComp-3LM / (2E)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]-4-(methylsulfanyl)but-2-enoic acid


Mass: 378.338 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H19N2O7PS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O

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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: 2.78 Å3/Da / Density % sol: 55.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Na-K phosphate buffer, 6-10 % PEG 6000, 0.25 M ammonium sulfate. 0.5 mM PLP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→48.9 Å / Num. obs: 53025 / % possible obs: 99.8 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.169 / Net I/σ(I): 8.8
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.435 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
CrystalCleardata reduction
CrystalCleardata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O7C

2o7c


Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.872 / SU B: 12.092 / SU ML: 0.248 / Cross valid method: THROUGHOUT / ESU R: 1.305 / ESU R Free: 0.332 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24635 2680 5.1 %RANDOM
Rwork0.1954 ---
obs0.19797 50074 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 34.138 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å2-0 Å2-0 Å2
2---0.14 Å20 Å2
3---0.34 Å2
Refinement stepCycle: 1 / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11849 0 96 64 12009
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01912202
X-RAY DIFFRACTIONr_bond_other_d0.0030.0211615
X-RAY DIFFRACTIONr_angle_refined_deg1.3241.96516564
X-RAY DIFFRACTIONr_angle_other_deg0.9363.00126616
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.39151570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.58323.366514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.219151898
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5241580
X-RAY DIFFRACTIONr_chiral_restr0.0680.21857
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02114018
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022832
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5463.4156300
X-RAY DIFFRACTIONr_mcbond_other1.5423.4146297
X-RAY DIFFRACTIONr_mcangle_it2.7375.1157862
X-RAY DIFFRACTIONr_mcangle_other2.7355.1157862
X-RAY DIFFRACTIONr_scbond_it1.2573.5825902
X-RAY DIFFRACTIONr_scbond_other1.2573.5835903
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2435.3198703
X-RAY DIFFRACTIONr_long_range_B_refined4.92627.05812922
X-RAY DIFFRACTIONr_long_range_B_other4.92527.06312920
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 194 -
Rwork0.241 3601 -
obs--100 %

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