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- PDB-1pff: Crystal Structure of Homocysteine alpha-, gamma-lyase at 1.8 Angstroms -

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Basic information

Entry
Database: PDB / ID: 1pff
TitleCrystal Structure of Homocysteine alpha-, gamma-lyase at 1.8 Angstroms
Componentsmethionine gamma-lyase
KeywordsLYASE / gamma-lyase / homocysteine / methionine
Function / homology
Function and homology information


carbon-sulfur lyase activity / methionine gamma-lyase / methionine gamma-lyase activity / transsulfuration / pyridoxal phosphate binding / cytoplasm
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
DI(HYDROXYETHYL)ETHER / L-methionine gamma-lyase
Similarity search - Component
Biological speciesTrichomonas vaginalis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsAllen, T.W. / Sridhar, V. / Prasad, S.G. / Han, Q. / Xu, M. / Tan, Y. / Hoffman, R.M. / Ramaswamy, S.
History
DepositionMay 26, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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)73,49126
Polymers71,8692
Non-polymers1,62224
Water6,107339
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)146,98152
Polymers143,7384
Non-polymers3,24448
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)166.634, 48.476, 75.606
Angle α, β, γ (deg.)90.00, 110.33, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-1615-

HOH

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Components

#1: Protein methionine gamma-lyase


Mass: 35934.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: O15565, methionine gamma-lyase
#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.23 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES/NaOH (ph 7.5), 100 mM MgCl2, 15% w/v MPEG 2000, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→32.5 Å / Num. obs: 19864

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Processing

Software
NameVersionClassification
REFMAC5.1.27refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E5F

1e5f


Resolution: 2.5→32.5 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.174 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 1.86 / ESU R: 0.147 / ESU R Free: 0.128
RfactorNum. reflection% reflectionSelection details
Rfree0.20837 1035 2.1 %RANDOM
Rwork0.17914 ---
all0.1792 ---
obs0.17975 19864 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.266 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å20 Å2-0.96 Å2
2--0.64 Å20 Å2
3----0.62 Å2
Refinement stepCycle: LAST / Resolution: 2.5→32.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5040 0 84 360 5484
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0215212
X-RAY DIFFRACTIONr_angle_refined_deg1.1391.9677011
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3415660
X-RAY DIFFRACTIONr_chiral_restr0.0830.2823
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023748
X-RAY DIFFRACTIONr_nbd_refined0.2180.22564
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2365
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.2137
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2070.257
X-RAY DIFFRACTIONr_mcbond_it0.5641.53293
X-RAY DIFFRACTIONr_mcangle_it1.07925306
X-RAY DIFFRACTIONr_scbond_it1.6831919
X-RAY DIFFRACTIONr_scangle_it2.8824.51701
LS refinement shellHighest resolution: 2.5 Å
Num. reflection% reflection
Rfree62 -
Rwork3083 -
obs7928 79.2 %

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