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- PDB-5x30: Crystal structure of Pseudomonas putida methionine gamma-lyase C1... -

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Basic information

Entry
Database: PDB / ID: 5x30
TitleCrystal structure of Pseudomonas putida methionine gamma-lyase C116H mutant with L-homocysteine intermediates.
Components(L-methionine gamma- ...) x 2
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-4LM / Chem-7XF / HYDROSULFURIC ACID / 2-AMINO-4-MERCAPTO-BUTYRIC ACID / L-methionine gamma-lyase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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
Revision 1.3Mar 6, 2024Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms

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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)172,2929
Polymers171,2914
Non-polymers1,0015
Water18,3931021
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19530 Å2
ΔGint-92 kcal/mol
Surface area46780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.753, 152.971, 80.586
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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L-methionine gamma- ... , 2 types, 4 molecules ACBD

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


Mass: 42936.738 Da / Num. of mol.: 2 / Mutation: C116H
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: 42708.621 Da / Num. of mol.: 2 / Mutation: C116H
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

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Non-polymers , 5 types, 1026 molecules

#3: Chemical ChemComp-HCS / 2-AMINO-4-MERCAPTO-BUTYRIC ACID / L-Homocysteine


Type: L-peptide linking / Mass: 135.185 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H9NO2S
#4: Chemical ChemComp-4LM / (2E)-2-{[(1E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}but-2-enoic acid


Mass: 330.230 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H15N2O7P
#5: Chemical ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE


Mass: 34.081 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2S
#6: 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.: 1 / Source method: obtained synthetically / Formula: C12H19N2O7PS
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1021 / 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: 2.77 Å3/Da / Density % sol: 55.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M Na-K phosphate buffer, 6-10% PEG 6000, 0.25M ammonium sulfate. 0.5mM PLP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Feb 4, 2014
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 208507 / % possible obs: 99.5 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 18.5
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 3.8 / % possible all: 97.9

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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: 1.7→20 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.817 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.087 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19508 10413 5 %RANDOM
Rwork0.16967 ---
obs0.17093 196805 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.41 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å2-
2---0.1 Å20 Å2
3----0.06 Å2
Refinement stepCycle: 1 / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11900 0 62 1021 12983
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01912243
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211656
X-RAY DIFFRACTIONr_angle_refined_deg1.4171.96516626
X-RAY DIFFRACTIONr_angle_other_deg0.95326712
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.02751575
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.3523.333519
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.454151893
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1491580
X-RAY DIFFRACTIONr_chiral_restr0.0830.21863
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02114076
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022859
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_it1.692.8056318
X-RAY DIFFRACTIONr_mcbond_other1.692.8056317
X-RAY DIFFRACTIONr_mcangle_it2.8194.1967887
X-RAY DIFFRACTIONr_mcangle_other2.8194.1977888
X-RAY DIFFRACTIONr_scbond_it1.9683.1065925
X-RAY DIFFRACTIONr_scbond_other1.9623.1065925
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2274.5598740
X-RAY DIFFRACTIONr_long_range_B_refined6.05423.50314320
X-RAY DIFFRACTIONr_long_range_B_other5.86223.14713824
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 756 -
Rwork0.251 14023 -
obs--97.68 %

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