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- PDB-5x2v: Crystal structure of Pseudomonas putida methionine gamma-lyase wi... -

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Basic information

Entry
Database: PDB / ID: 5x2v
TitleCrystal structure of Pseudomonas putida methionine gamma-lyase wild type without sulfate ion
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
L-methionine gamma-lyase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 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


Theoretical massNumber of molelcules
Total (without water)171,6074
Polymers171,6074
Non-polymers00
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19080 Å2
ΔGint-98 kcal/mol
Surface area47390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.219, 153.535, 80.579
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: 42901.734 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 55.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
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 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→48.75 Å / Num. obs: 75515 / % possible obs: 97.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.157 / Net I/σ(I): 7
Reflection shellResolution: 2.4→2.48 Å / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 3.4 / % possible all: 91.2

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
CrystalCleardata reduction
CrystalCleardata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O7C

2o7c


Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.86 / SU B: 10.412 / SU ML: 0.234 / Cross valid method: THROUGHOUT / ESU R: 0.386 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2756 3732 5 %RANDOM
Rwork0.21604 ---
obs0.21907 70404 98.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.443 Å2
Baniso -1Baniso -2Baniso -3
1-1.81 Å20 Å2-0 Å2
2---1.06 Å2-0 Å2
3----0.75 Å2
Refinement stepCycle: 1 / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11891 0 0 48 11939
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01912143
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211594
X-RAY DIFFRACTIONr_angle_refined_deg1.5891.96916487
X-RAY DIFFRACTIONr_angle_other_deg0.8333.00226473
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.07451560
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.08823.372513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.625151878
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2421580
X-RAY DIFFRACTIONr_chiral_restr0.1290.21855
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02113938
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022806
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_it2.1112.9256276
X-RAY DIFFRACTIONr_mcbond_other2.112.9256275
X-RAY DIFFRACTIONr_mcangle_it3.6134.3857824
X-RAY DIFFRACTIONr_mcangle_other3.6134.3857825
X-RAY DIFFRACTIONr_scbond_it1.8523.125867
X-RAY DIFFRACTIONr_scbond_other1.8513.125867
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0774.6148663
X-RAY DIFFRACTIONr_long_range_B_refined6.56323.53413413
X-RAY DIFFRACTIONr_long_range_B_other6.56323.53913408
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 271 -
Rwork0.312 4723 -
obs--91.05 %

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