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- PDB-1e5f: METHIONINE GAMMA-LYASE (MGL) FROM TRICHOMONAS VAGINALIS -

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Basic information

Entry
Database: PDB / ID: 1e5f
TitleMETHIONINE GAMMA-LYASE (MGL) FROM TRICHOMONAS VAGINALIS
ComponentsMETHIONINE GAMMA-LYASE
KeywordsLYASE / METHIONINE BIOSYNTHESIS / PLP-DEPENDENT ENZYMES / C-S GAMMA LYASE
Function / homology
Function and homology information


methionine gamma-lyase / methionine gamma-lyase activity / transsulfuration / pyridoxal phosphate binding
Similarity search - Function
L-methionine gamma-lyase / 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 ...L-methionine gamma-lyase / 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
PYRIDOXAL-5'-PHOSPHATE / L-methionine gamma-lyase
Similarity search - Component
Biological speciesTRICHOMONAS VAGINALIS (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsGoodall, G. / Mottram, J.C. / Coombs, G.H. / Lapthorn, A.J.
CitationJournal: To be Published
Title: The Structure and Proposed Catalytic Mechanism of Methionine Gamma-Lyase
Authors: Goodall, G. / Mottram, J.C. / Coombs, G.H. / Lapthorn, A.J.
History
DepositionJul 25, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2001Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2011Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Nov 14, 2012Group: Database references
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,46211
Polymers88,2992
Non-polymers1,1639
Water11,620645
1
A: METHIONINE GAMMA-LYASE
B: METHIONINE GAMMA-LYASE
hetero molecules

A: METHIONINE GAMMA-LYASE
B: METHIONINE GAMMA-LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,92422
Polymers176,5994
Non-polymers2,32618
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_655-x+y+1,y,-z+1/31
Buried area22960 Å2
ΔGint-266.1 kcal/mol
Surface area45170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.258, 88.258, 217.849
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.68456, -0.00368, -0.72894), (0.00077, -0.99999, 0.00432), (-0.72895, 0.00239, 0.68456)
Vector: 100.83318, 89.38553, 43.5929)

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Components

#1: Protein METHIONINE GAMMA-LYASE / / MGL


Mass: 44149.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRICHOMONAS VAGINALIS (eukaryote) / Strain: G3 / Cellular location: CYTOPLASM / Gene: MGL1 / Plasmid: PQE60 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15 / References: UniProt: O15564, methionine gamma-lyase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 645 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A,B: SOME CHANGES TO SEQUENCE INTRODUCED IN EXPRESSION CONSTRUCT. RESIDUES 397 TO 404 ADDED AS HIS TAG.
Sequence detailsSOME CHANGES TO SEQUENCE INTRODUCED IN EXPRESSION CONSTRUCT

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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: 2.85 Å3/Da / Density % sol: 50.8 %
Crystal growpH: 5.6
Details: 3.2M AMMONIUM SULPHATE, 0.2M LISO4, 0.1M CITRATE PH5.6, pH 5.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 1.1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1998
RadiationMonochromator: SI 111 CHANNEL CUT MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.18→28.9 Å / Num. obs: 49696 / % possible obs: 98.6 % / Redundancy: 2.5 % / Biso Wilson estimate: 29 Å2 / Rsym value: 0.067 / Net I/σ(I): 12.5
Reflection shellResolution: 2.18→2.26 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.365 / % possible all: 97.2

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CL1

1cl1


Resolution: 2.18→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.22187 / ESU R Free: 0.1852
RfactorNum. reflection% reflectionSelection details
Rfree0.212 2368 5 %RANDOM
Rwork0.162 ---
obs-44982 98.6 %-
Displacement parametersBiso mean: 31.4 Å2
Refinement stepCycle: LAST / Resolution: 2.18→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5909 0 66 645 6620
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.02
X-RAY DIFFRACTIONp_angle_d0.0410.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0460.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.6632
X-RAY DIFFRACTIONp_mcangle_it2.3033
X-RAY DIFFRACTIONp_scbond_it2.2312
X-RAY DIFFRACTIONp_scangle_it3.1323
X-RAY DIFFRACTIONp_plane_restr0.02480.03
X-RAY DIFFRACTIONp_chiral_restr0.1410.15
X-RAY DIFFRACTIONp_singtor_nbd0.1870.3
X-RAY DIFFRACTIONp_multtor_nbd0.260.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1540.3
X-RAY DIFFRACTIONp_planar_tor4.97
X-RAY DIFFRACTIONp_staggered_tor15.715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor30.920
X-RAY DIFFRACTIONp_special_tor15

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