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- PDB-3mkj: Methionine gamma-lyase from Citrobacter freundii with pyridoximin... -

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Basic information

Entry
Database: PDB / ID: 3mkj
TitleMethionine gamma-lyase from Citrobacter freundii with pyridoximine-5'-phosphate
ComponentsMethionine gamma-lyase
KeywordsLYASE / Pyridoxal-5'-phosphate / PLP-dependent enzyme / X-ray damage
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
Chem-PZP / L-methionine gamma-lyase
Similarity search - Component
Biological speciesCitrobacter freundii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsRevtovich, S.V. / Nikulin, A.D. / Morozova, E.A. / Demidkina, T.V.
CitationJournal: Biochim.Biophys.Acta / Year: 2011
Title: Exploring methionine gamma-lyase structure-function relationship via microspectrophotometry and X-ray crystallography
Authors: Ronda, L. / Bazhulina, N.P. / Morozova, E.A. / Revtovich, S.V. / Chekhov, V.O. / Nikulin, A.D. / Demidkina, T.V. / Mozzarelli, A.
History
DepositionApr 15, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 5, 2014Group: Database references
Revision 1.3Nov 1, 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 / diffrn_source / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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 1.4Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)43,2472
Polymers43,0011
Non-polymers2461
Water5,747319
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)172,9888
Polymers172,0034
Non-polymers9854
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 area19430 Å2
ΔGint-117 kcal/mol
Surface area48270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.690, 122.800, 128.040
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-433-

HOH

21A-439-

HOH

31A-717-

HOH

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Components

#1: Protein Methionine gamma-lyase


Mass: 43000.801 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-PZP / [5-hydroxy-4-(iminomethyl)-6-methyl-pyridin-3-yl]methyl dihydrogen phosphate / pyridoximine-5'-phosphate


Mass: 246.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H11N2O5P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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: 2.59 Å3/Da / Density % sol: 52.53 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 37% MMEPEG 2000, 200MM ammonium sulfate, 50MM TRIS-HCL, 0.2MM PLP, 0.2MM 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: Apr 3, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.843 Å / Relative weight: 1
ReflectionResolution: 1.65→20 Å / Num. all: 50624 / Num. obs: 50624 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 17.72
Reflection shellResolution: 1.65→1.7 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 4.7 / Num. unique all: 2663 / % possible all: 59

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.6_289)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RFV

2rfv


Resolution: 1.65→14.905 Å / Occupancy max: 1 / Occupancy min: 0.24 / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2324 2590 5.12 %RANDOM
Rwork0.1961 ---
obs0.198 50588 93.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 65.007 Å2 / ksol: 0.417 e/Å3
Displacement parametersBiso max: 85.37 Å2 / Biso mean: 27.226 Å2 / Biso min: 8.98 Å2
Baniso -1Baniso -2Baniso -3
1--4.872 Å20 Å20 Å2
2--2.249 Å20 Å2
3---2.623 Å2
Refinement stepCycle: LAST / Resolution: 1.65→14.905 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2918 0 16 319 3253
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073010
X-RAY DIFFRACTIONf_angle_d1.0634091
X-RAY DIFFRACTIONf_chiral_restr0.073473
X-RAY DIFFRACTIONf_plane_restr0.005533
X-RAY DIFFRACTIONf_dihedral_angle_d20.7941098
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.680.5470.47491195834
1.68-1.7120.3741520.3382455260792
1.712-1.7470.3331410.292506264795
1.747-1.7850.2951360.2612541267795
1.785-1.8270.311220.2622593271596
1.827-1.8720.3021390.242559269897
1.872-1.9230.2741320.2312622275497
1.923-1.9790.2581460.232595274198
1.979-2.0430.2441490.2292627277698
2.043-2.1160.2831490.2152653280298
2.116-2.20.2361540.2022592274698
2.2-2.30.2691350.1912659279499
2.3-2.4210.2251540.1882657281199
2.421-2.5720.241640.1912660282499
2.572-2.7690.2441060.1852695280199
2.769-3.0460.231310.1842700283199
3.046-3.4820.1991480.172695284399
3.482-4.3680.1741330.152707284097
4.368-14.9050.1811520.1692571272390

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