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- PDB-7f1v: Crystal structure of Pseudomonas putida methionine gamma-lyase Q3... -

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Basic information

Entry
Database: PDB / ID: 7f1v
TitleCrystal structure of Pseudomonas putida methionine gamma-lyase Q349S mutant with L-homocysteine intermediates
Components(L-methionine gamma-lyase) x 2
KeywordsLYASE / Pseudomonas putida / methionine gamma-lyase / PLP enzyme
Function / homology
Function and homology information


homocysteine desulfhydrase / homocysteine desulfhydrase activity / 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 / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Chem-7XF / 2-AMINO-4-MERCAPTO-BUTYRIC ACID / L-methionine gamma-lyase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsOkawa, A. / Handa, H. / Yasuda, E. / Murota, M. / Kudo, D. / Tamura, T. / Shiba, T. / Inagaki, K.
CitationJournal: J.Biosci.Bioeng. / Year: 2022
Title: Characterization and application of l-methionine gamma-lyase Q349S mutant enzyme with an enhanced activity toward l-homocysteine.
Authors: Okawa, A. / Handa, H. / Yasuda, E. / Murota, M. / Kudo, D. / Tamura, T. / Shiba, T. / Inagaki, K.
History
DepositionJun 9, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Mar 13, 2024Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)171,8547
Polymers170,9874
Non-polymers8683
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19140 Å2
ΔGint-98 kcal/mol
Surface area45570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.075, 152.299, 80.508
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: 42632.566 Da / Num. of mol.: 2 / Mutation: Q349S
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: Protein L-methionine gamma-lyase / MGL / Homocysteine desulfhydrase / L-methioninase


Mass: 42860.684 Da / Num. of mol.: 2 / Mutation: Q349S
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
#3: Chemical ChemComp-7XF / (2~{S})-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]-4-sulfanyl-butanoic acid


Mass: 366.327 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N2O7PS / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-HCS / 2-AMINO-4-MERCAPTO-BUTYRIC ACID / L-Homocysteine


Type: L-peptide linking / Mass: 135.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO2S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.76 Å3/Da / Density % sol: 55.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M NA-K PHOSPHATE BUFFER, pH 5.6-5.8, 6-9 % PEG 6000, 0.25 M AMMONIUM SULFATE. 0.5 MM PLP, 0.5%(v/v) 2-mercaptoethanol
PH range: 5.6-5.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 19, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 90099 / % possible obs: 97.5 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 6.5
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4248 / % possible all: 95.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O7C

2o7c


Resolution: 2.25→19.97 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.922 / SU B: 6.208 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.303 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22658 3961 5 %RANDOM
Rwork0.18782 ---
obs0.18978 75074 87.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.614 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.25→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11849 0 54 198 12101
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01912161
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211577
X-RAY DIFFRACTIONr_angle_refined_deg1.4181.96716512
X-RAY DIFFRACTIONr_angle_other_deg0.9793.00126544
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3951568
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.59523.32509
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.919151882
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9611580
X-RAY DIFFRACTIONr_chiral_restr0.0830.21856
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02113964
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022818
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_it2.0083.786293
X-RAY DIFFRACTIONr_mcbond_other2.0083.7796289
X-RAY DIFFRACTIONr_mcangle_it3.3465.667854
X-RAY DIFFRACTIONr_mcangle_other3.3465.6597853
X-RAY DIFFRACTIONr_scbond_it2.0634.0655868
X-RAY DIFFRACTIONr_scbond_other2.0554.0645867
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4495.9958659
X-RAY DIFFRACTIONr_long_range_B_refined5.68729.70712948
X-RAY DIFFRACTIONr_long_range_B_other5.68529.71612922
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.254→2.312 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 207 -
Rwork0.249 3633 -
obs--58.88 %

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