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- PDB-1gc2: CRYSTAL STRUCTURE OF THE PYRIDOXAL-5'-PHOSPHATE DEPENDENT L-METHI... -

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Basic information

Entry
Database: PDB / ID: 1gc2
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: 2 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
Water21,4201189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16280 Å2
ΔGint-88 kcal/mol
Surface area46060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.576, 133.576, 213.675
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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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.: 1189 / 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: 55.69 %
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-IDChemical formulaDetails
115 %PEG60001reservoir
2250 mM1reservoirNaCl
3200 mMMES-NaOH1reservoirpH6.5
40.5 mMPLP1reservoir
50.5 %2-mercaptoethanol1drop
610-20 mg/mlprotein1drop
720 mMsodium phosphate1droppH7.2
80.5 mMPLP1drop
90.5 %2-mercaptoethanol1drop

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONSPring-8 BL45XU11.0025
SYNCHROTRONSPring-8 BL45XU20.9485
SYNCHROTRONSPring-8 BL45XU30.9503
Detector
TypeIDDetector
RIGAKU RAXIS IV++1IMAGE PLATE
RIGAKU RAXIS IV++2IMAGE PLATE
RIGAKU RAXIS IV++3IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.00251
20.94851
30.95031
ReflectionHighest resolution: 1.7 Å / Num. all: 1016993 / Num. obs: 130168 / % possible obs: 99.7 % / Biso Wilson estimate: 19.8 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 7.9
Reflection
*PLUS
Highest resolution: 2 Å / Num. measured all: 1016993 / Rmerge(I) obs: 0.079

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2→83.43 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 320661.45 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.243 12353 10 %RANDOM
Rwork0.211 ---
obs0.211 123918 94.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.34 Å2 / ksol: 0.371 e/Å3
Displacement parametersBiso mean: 37.1 Å2
Baniso -1Baniso -2Baniso -3
1--4.75 Å20 Å20 Å2
2---4.75 Å20 Å2
3---9.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2→83.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11255 0 0 1189 12444
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
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: 2→2.13 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.297 1969 10.1 %
Rwork0.268 17431 -
obs--90.4 %
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: 0.243 / Rfactor Rwork: 0.211
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.26
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.544
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.713
LS refinement shell
*PLUS
Rfactor Rfree: 0.297 / Rfactor Rwork: 0.268 / Rfactor obs: 0.268

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