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- PDB-2o7c: Crystal structure of L-methionine-lyase from Pseudomonas -

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Basic information

Entry
Database: PDB / ID: 2o7c
TitleCrystal structure of L-methionine-lyase from Pseudomonas
ComponentsMethionine gamma-lyase
KeywordsLYASE / PLP / Methionine / Cancer
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 / 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 ...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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMisaki, S. / Takimoto, A. / Takakura, T. / Yoshioka, T. / Yamashita, M. / Tamura, T. / Tanaka, H. / Inagaki, K.
CitationJournal: J.Biochem.(Tokyo) / Year: 2007
Title: Structure of the antitumour enzyme L-methionine gamma-lyase from Pseudomonas putida at 1.8 A resolution
Authors: Kudou, D. / Misaki, S. / Yamashita, M. / Tamura, T. / Takakura, T. / Yoshioka, T. / Yagi, S. / Hoffman, R.M. / Takimoto, A. / Esaki, N. / Inagaki, K.
History
DepositionDec 10, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)171,9918
Polymers171,6074
Non-polymers3844
Water12,953719
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20610 Å2
ΔGint-174 kcal/mol
Surface area45100 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)133.129, 133.129, 215.243
Angle α, β, γ (deg.)90, 90, 90
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
Methionine gamma-lyase / L-methioninase


Mass: 42901.734 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Plasmid: PMGL1204 / Production host: Escherichia coli (E. coli) / References: UniProt: P13254, methionine gamma-lyase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 719 / 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: 55.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 20% PEG 6000, 0.1M ammonium sulfate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL24XU / Wavelength: 0.834 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Oct 10, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.834 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. all: 176570 / Num. obs: 173038 / % possible obs: 98 % / Redundancy: 14.4 % / Rmerge(I) obs: 0.075

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Processing

Software
NameVersionClassification
HKL-2000data collection
X-PLORmodel building
X-PLOR3.851refinement
HKL-2000data reduction
HKL-2000data scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→40 Å / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1
RfactorNum. reflectionSelection details
Rfree0.224 -RANDOM
Rwork0.204 --
all-176570 -
obs-173038 -
Refinement stepCycle: LAST / Resolution: 1.7→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12044 0 20 719 12783
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.525
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d19.81
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.44
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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