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- PDB-4oma: The crystal structure of methionine gamma-lyase from Citrobacter ... -

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Basic information

Entry
Database: PDB / ID: 4oma
TitleThe crystal structure of methionine gamma-lyase from Citrobacter freundii in complex with L-cycloserine pyridoxal-5'-phosphate
Componentsmethionine gamma-lyase
KeywordsLYASE / aminotransferase class I and II / methionine
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
Chem-LCS / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / L-methionine gamma-lyase / :
Similarity search - Component
Biological speciesCitrobacter freundii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsRevtovich, S.V. / Nikulin, A.D. / Morozova, E.A. / Demidkina, T.V.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Pre-steady-state Kinetic and Structural Analysis of Interaction of Methionine gamma-Lyase from Citrobacter freundii with Inhibitors.
Authors: Kuznetsov, N.A. / Faleev, N.G. / Kuznetsova, A.A. / Morozova, E.A. / Revtovich, S.V. / Anufrieva, N.V. / Nikulin, A.D. / Fedorova, O.S. / Demidkina, T.V.
History
DepositionJan 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2014Group: Database references
Revision 1.2Jan 21, 2015Group: Database references
Revision 1.3Sep 20, 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_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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8167
Polymers42,9371
Non-polymers8796
Water4,792266
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)175,26428
Polymers171,7474
Non-polymers3,51724
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 area27720 Å2
ΔGint-137 kcal/mol
Surface area46780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.270, 122.890, 126.610
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-694-

HOH

21A-756-

HOH

31A-757-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein methionine gamma-lyase /


Mass: 42936.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrobacter freundii (bacteria) / Gene: H922_06139, megl / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: R1FPL7, UniProt: Q84AR1*PLUS, methionine gamma-lyase

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Non-polymers , 5 types, 272 molecules

#2: Chemical ChemComp-LCS / [5-hydroxy-6-methyl-4-({[(4E)-3-oxo-1,2-oxazolidin-4-ylidene]amino}methyl)pyridin-3-yl]methyl dihydrogen phosphate


Mass: 331.219 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H14N3O7P
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.55 Å3/Da / Density % sol: 51.74 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 5% PEG2000 MME, 50 mM Tris-HCl, 0.2 mM PLP, 0.25% DTT, pH 8.5, soaked in 50 mM L-cycloserine for 7 minutes, 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: Nov 11, 2005
RadiationMonochromator: sagitally focused Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.843 Å / Relative weight: 1
ReflectionResolution: 1.6→15 Å / Num. all: 55080 / Num. obs: 55080 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 26.8 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 17.28
Reflection shellResolution: 1.6→1.65 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 3.6 / Num. unique all: 4606 / % possible all: 94.3

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASESphasing
REFMAC5.8.0049refinement
PROCESSdata reduction
PROCESSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2RFV

2rfv


Resolution: 1.6→15 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.964 / SU B: 7.606 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.086 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.197 2893 5.1 %RANDOM
Rwork0.139 ---
all0.142 53896 --
obs0.142 53896 97.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.688 Å2
Baniso -1Baniso -2Baniso -3
1-5.51 Å2-0 Å2-0 Å2
2---2.81 Å20 Å2
3----2.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.206 Å
Refinement stepCycle: LAST / Resolution: 1.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2993 0 57 266 3316
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0193177
X-RAY DIFFRACTIONr_bond_other_d0.0030.023066
X-RAY DIFFRACTIONr_angle_refined_deg1.9431.9854314
X-RAY DIFFRACTIONr_angle_other_deg1.0143.0047060
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.355414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.69624.308130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.97915532
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4271518
X-RAY DIFFRACTIONr_chiral_restr0.1440.2495
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213592
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02683
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.7572.5961609
X-RAY DIFFRACTIONr_mcbond_other4.7382.5921605
X-RAY DIFFRACTIONr_mcangle_it5.9933.9122014
X-RAY DIFFRACTIONr_mcangle_other5.963.912013
X-RAY DIFFRACTIONr_scbond_it6.3763.0231566
X-RAY DIFFRACTIONr_scbond_other6.3743.0251567
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.3644.372290
X-RAY DIFFRACTIONr_long_range_B_refined7.55522.7073784
X-RAY DIFFRACTIONr_long_range_B_other7.24822.2043676
X-RAY DIFFRACTIONr_rigid_bond_restr7.2636240
X-RAY DIFFRACTIONr_sphericity_free48.856564
X-RAY DIFFRACTIONr_sphericity_bonded22.14956381
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 200 -
Rwork0.275 3808 -
obs-4008 94.28 %

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