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- PDB-3jwb: Crystal structure of L-methionine gamma-lyase from Citrobacter fr... -

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Basic information

Entry
Database: PDB / ID: 3jwb
TitleCrystal structure of L-methionine gamma-lyase from Citrobacter freundii with norleucine
ComponentsMethionine gamma-lyase
KeywordsLYASE / PYRIDOXAL-5'-PHOSPHATE / PLP-DEPENDENT ENZYME
Function / homology
Function and homology information


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
NORLEUCINE / DI(HYDROXYETHYL)ETHER / L-methionine gamma-lyase
Similarity search - Component
Biological speciesCitrobacter freundii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsRevtovish, S.V. / Nikulin, A.D. / Morozova, E.A. / Demidkina, T.V.
CitationJournal: Biochemistry Mosc. / Year: 2011
Title: Three-dimensional structures of noncovalent complexes of Citrobacter freundii methionine gamma-lyase with substrates.
Authors: Revtovich, S.V. / Morozova, E.A. / Khurs, E.N. / Zakomirdina, L.N. / Nikulin, A.D. / Demidkina, T.V. / Khomutov, R.M.
History
DepositionSep 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 5, 2014Group: Database references
Revision 1.3Oct 21, 2020Group: Data collection / Derived calculations
Category: diffrn_source / reflns_shell ...diffrn_source / reflns_shell / struct_conn / struct_site
Item: _diffrn_source.pdbx_synchrotron_site / _reflns_shell.Rmerge_I_obs ..._diffrn_source.pdbx_synchrotron_site / _reflns_shell.Rmerge_I_obs / _reflns_shell.number_unique_all / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_Rsym_value / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methionine gamma-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6305
Polymers43,1811
Non-polymers4504
Water5,783321
1
A: Methionine gamma-lyase
hetero molecules

A: Methionine gamma-lyase
hetero molecules

A: Methionine gamma-lyase
hetero molecules

A: Methionine gamma-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,52220
Polymers172,7244
Non-polymers1,79816
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area23760 Å2
ΔGint-79 kcal/mol
Surface area46340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.76, 123.15, 127.62
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-406-

HOH

21A-512-

HOH

31A-595-

HOH

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Components

#1: Protein Methionine gamma-lyase /


Mass: 43180.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrobacter freundii (bacteria) / Gene: megL / Plasmid: PET-MGL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q84AR1, methionine gamma-lyase
#2: Chemical ChemComp-NLE / NORLEUCINE / Norleucine


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 321 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THERE IS AN ERROR IN THE DATABASE SEQUENCE.

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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: 2.58 Å3/Da / Density % sol: 52.37 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 5% MMEPEG 2000, 50MM TRIS-HCl, 0.2MM PLP, 0.25% DTT , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.843 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 19, 2005 / Details: mirrors
RadiationMonochromator: Si(111), horizontally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.843 Å / Relative weight: 1
ReflectionResolution: 1.63→20 Å / Num. all: 54913 / Num. obs: 54913 / % possible obs: 92.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 26.9 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 11.35
Reflection shellResolution: 1.63→1.67 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 3368 / Rsym value: 0.339 / % possible all: 81.6

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.4_4)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RFV

2rfv


Resolution: 1.63→20 Å / SU ML: 0.01 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2172 2747 5 %RANDOM
Rwork0.1599 ---
obs0.1627 54913 97.23 %-
all-54913 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80.739 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.6719 Å20 Å20 Å2
2---6.0111 Å20 Å2
3----0.6608 Å2
Refinement stepCycle: LAST / Resolution: 1.63→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3009 0 30 321 3360
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043172
X-RAY DIFFRACTIONf_angle_d0.9194313
X-RAY DIFFRACTIONf_dihedral_angle_d15.5791176
X-RAY DIFFRACTIONf_chiral_restr0.063499
X-RAY DIFFRACTIONf_plane_restr0.004559
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6264-1.65440.28841180.21782238X-RAY DIFFRACTION85
1.6544-1.68450.28121320.18582500X-RAY DIFFRACTION94
1.6845-1.71690.25131320.16852516X-RAY DIFFRACTION95
1.7169-1.75190.24351330.16432527X-RAY DIFFRACTION96
1.7519-1.78990.23011350.16122555X-RAY DIFFRACTION95
1.7899-1.83150.24281340.16692544X-RAY DIFFRACTION96
1.8315-1.87730.25061340.16282553X-RAY DIFFRACTION97
1.8773-1.9280.25151380.16152613X-RAY DIFFRACTION98
1.928-1.98470.25371380.16232618X-RAY DIFFRACTION98
1.9847-2.04870.2221380.16242625X-RAY DIFFRACTION98
2.0487-2.12180.23881390.15982651X-RAY DIFFRACTION99
2.1218-2.20660.23231390.16312626X-RAY DIFFRACTION99
2.2066-2.30690.22611390.15592646X-RAY DIFFRACTION99
2.3069-2.42830.19591410.1622677X-RAY DIFFRACTION99
2.4283-2.580.25391410.15312688X-RAY DIFFRACTION100
2.58-2.77870.20411400.15982664X-RAY DIFFRACTION100
2.7787-3.05720.21331420.16532699X-RAY DIFFRACTION100
3.0572-3.49710.22461440.15372725X-RAY DIFFRACTION100
3.4971-4.39660.16221450.13732748X-RAY DIFFRACTION100
4.3966-18.75770.19121450.16032753X-RAY DIFFRACTION97

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