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- PDB-5m3z: Crystal structure of Citrobacter freundii methionine gamma-lyase ... -

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Basic information

Entry
Database: PDB / ID: 5m3z
TitleCrystal structure of Citrobacter freundii methionine gamma-lyase with C115H replacement in the complex with L-norleucine
ComponentsMethionine gamma-lyase
KeywordsLYASE / methionine gamma-lyase / C115H substitution / L-norleucine
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 / TRIETHYLENE GLYCOL / PYRIDOXAL-5'-PHOSPHATE / 2-[O-PHOSPHONOPYRIDOXYL]-AMINO-HEXANOIC ACID / L-methionine gamma-lyase
Similarity search - Component
Biological speciesCitrobacter freundii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsRevtovich, S.V. / Nikulin, A.D. / Anufrieva, N.V. / Morozova, E.A. / Demidkina, T.V.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
RSF15-14-00009 Russian Federation
CitationJournal: Biochim. Biophys. Acta / Year: 2017
Title: Crystal structure of mutant form Cys115His of Citrobacter freundii methionine gamma-lyase complexed with l-norleucine.
Authors: Revtovich, S.V. / Morozova, E.A. / Kulikova, V.V. / Anufrieva, N.V. / Osipova, T.I. / Koval, V.S. / Nikulin, A.D. / Demidkina, T.V.
History
DepositionOct 17, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 17, 2024Group: 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

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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)43,8795
Polymers42,9881
Non-polymers8914
Water6,233346
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)175,51420
Polymers171,9514
Non-polymers3,56316
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area23590 Å2
ΔGint-102 kcal/mol
Surface area46010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.513, 123.019, 127.577
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-504-

HOH

21A-664-

HOH

31A-726-

HOH

41A-750-

HOH

51A-795-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Methionine gamma-lyase


Mass: 42987.805 Da / Num. of mol.: 1 / Mutation: C115H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrobacter freundii (bacteria) / Gene: AN672_11005, HMPREF3212_02785, TN42_08855, TO64_18625 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0A0A5P8W7, methionine gamma-lyase

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Non-polymers , 5 types, 350 molecules

#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-NLE / NORLEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-PY6 / 2-[O-PHOSPHONOPYRIDOXYL]-AMINO-HEXANOIC ACID / VITAMIN B6 COMPLEXED WITH 2-AMINO-HEXANOIC ACID


Mass: 362.315 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H23N2O7P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 2.58 Å3/Da / Density % sol: 52.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: MGL 20mg/ml, PEG MME 2000 37.5%, 50 ml TrisHCl, 25mM DTT, 0.2 mM PLP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.95372 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 78132 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Net I/σ(I): 14.9
Reflection shellResolution: 1.45→1.47 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.8 / CC1/2: 0.569 / % possible all: 95.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RFV

2rfv


Resolution: 1.45→88.56 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.975 / SU B: 3.109 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16934 3806 4.9 %RANDOM
Rwork0.12832 ---
obs0.13033 74318 98.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.214 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å2-0 Å20 Å2
2--0.71 Å2-0 Å2
3----0.92 Å2
Refinement stepCycle: 1 / Resolution: 1.45→88.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2992 0 58 346 3396
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0193237
X-RAY DIFFRACTIONr_bond_other_d0.0040.023117
X-RAY DIFFRACTIONr_angle_refined_deg1.8331.9844415
X-RAY DIFFRACTIONr_angle_other_deg1.2553.0047181
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3275429
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.80124.328134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.315537
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7551518
X-RAY DIFFRACTIONr_chiral_restr0.130.2508
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213686
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02707
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_it4.2982.3321632
X-RAY DIFFRACTIONr_mcbond_other4.2482.331631
X-RAY DIFFRACTIONr_mcangle_it4.9663.5022044
X-RAY DIFFRACTIONr_mcangle_other4.973.5032045
X-RAY DIFFRACTIONr_scbond_it5.782.7591604
X-RAY DIFFRACTIONr_scbond_other5.7792.7591605
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.9973.9922356
X-RAY DIFFRACTIONr_long_range_B_refined6.45120.7343960
X-RAY DIFFRACTIONr_long_range_B_other6.37519.963751
X-RAY DIFFRACTIONr_rigid_bond_restr6.04536352
X-RAY DIFFRACTIONr_sphericity_free29.771571
X-RAY DIFFRACTIONr_sphericity_bonded20.35656554
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 267 -
Rwork0.289 5339 -
obs--96.99 %

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