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- PDB-1gc0: CRYSTAL STRUCTURE OF THE PYRIDOXAL-5'-PHOSPHATE DEPENDENT L-METHI... -

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Basic information

Entry
Database: PDB / ID: 1gc0
TitleCRYSTAL STRUCTURE OF THE PYRIDOXAL-5'-PHOSPHATE DEPENDENT L-METHIONINE GAMMA-LYASE FROM PSEUDOMONAS PUTIDA
ComponentsMETHIONINE 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 / SYNCHROTRON / Resolution: 1.7 Å
AuthorsMotoshima, H. / Inagaki, K. / Kumasaka, T. / Furuichi, M. / Inoue, H. / Tamura, T. / Esaki, N. / Soda, K. / Tanaka, N. / Yamamoto, M. / Tanaka, H.
Citation
Journal: J.Biochem. / Year: 2000
Title: Crystal structure of the pyridoxal 5'-phosphate dependent L-methionine gamma-lyase from Pseudomonas putida.
Authors: Motoshima, H. / Inagaki, K. / Kumasaka, T. / Furuichi, M. / Inoue, H. / Tamura, T. / Esaki, N. / Soda, K. / Tanaka, N. / Yamamoto, M. / Tanaka, H.
#1: Journal: J.BIOCHEM.(TOKYO) / Year: 1995
Title: Structural analysis of the L-methionine gamma-lyase gene from Pseudomonas putida.
Authors: Inoue, H. / Inagaki, K. / Sugimoto, M. / Esaki, N. / Soda, K. / Tanaka, H.
#2: Journal: J.Mol.Biol. / Year: 1996
Title: Crystal structure of the pyridoxal-5'-phosphate dependent cystathionine beta-lyase from Escherichia coli at 1.83 A.
Authors: Clausen, T. / Huber, R. / Laber, B. / Pohlenz, H.D. / Messerschmidt, A.
#3: Journal: Embo J. / Year: 1998
Title: Crystal structure of Escherichia coli cystathionine gamma-synthase at 1.5 A resolution.
Authors: Clausen, T. / Huber, R. / Prade, L. / Wahl, M.C. / Messerschmidt, A.
History
DepositionJul 6, 2000Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 8, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2019Group: Data collection / Database references / Derived calculations
Category: citation / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: METHIONINE GAMMA-LYASE
B: METHIONINE GAMMA-LYASE
C: METHIONINE GAMMA-LYASE
D: METHIONINE GAMMA-LYASE


Theoretical massNumber of molelcules
Total (without water)171,6074
Polymers171,6074
Non-polymers00
Water22,6631258
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15700 Å2
ΔGint-88 kcal/mol
Surface area46550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.861, 81.030, 81.282
Angle α, β, γ (deg.)70.56, 63.17, 63.38
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
METHIONINE GAMMA-LYASE


Mass: 42901.734 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Pseudomonas putida (bacteria) / References: UniProt: P13254, methionine gamma-lyase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1258 / 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: 2.2 Å3/Da / Density % sol: 44.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 %PEG60001reservoir
2250 mMammonium sulfate1reservoir
3200 mMTris-HCl1reservoirpH8.5
40.5 mMPLP1reservoir
50.5 %2-mercaptoethanol1reservoir
610-20 mg/mlprotein1drop
720 mMsodium phosphate1droppH7.2
80.5 mMPLP1drop
90.5 %2-mercaptoethanol1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1.02
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionHighest resolution: 1.7 Å / Num. all: 263490 / Num. obs: 144898 / % possible obs: 90.8 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 28.5
Reflection
*PLUS
Rmerge(I) obs: 0.037

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Processing

SoftwareName: CNS / Version: 0.9 / Classification: refinement
RefinementResolution: 1.7→71.46 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1463068.71 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.236 14638 10 %RANDOM
Rwork0.21 ---
obs0.21 146717 91 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.95 Å2 / ksol: 0.381 e/Å3
Displacement parametersBiso mean: 20.7 Å2
Baniso -1Baniso -2Baniso -3
1-2.06 Å20.04 Å20.92 Å2
2---0.63 Å2-1.85 Å2
3----1.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.05 Å
Refinement stepCycle: LAST / Resolution: 1.7→71.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10795 0 0 1258 12053
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.27 2324 9.9 %
Rwork0.239 21179 -
obs--87.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER.TOP
Refinement
*PLUS
Rfactor obs: 0.211 / Rfactor Rfree: 0.238 / Rfactor Rwork: 0.211
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.237
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.13
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.72
LS refinement shell
*PLUS
Rfactor Rfree: 0.27 / Rfactor Rwork: 0.239 / Rfactor obs: 0.239

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