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- PDB-6lxu: Crystal structure of methionine gamma-lyase from Fusobacterium nu... -

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Basic information

Entry
Database: PDB / ID: 6lxu
TitleCrystal structure of methionine gamma-lyase from Fusobacterium nucleatum
ComponentsL-methionine gamma-lyase
KeywordsLYASE / L-Methionine gamma-lyase
Function / homology
Function and homology information


L-cysteine desulfidase / carbon-sulfur lyase activity / homocysteine desulfhydrase activity / homocysteine desulfhydrase / methionine gamma-lyase / methionine gamma-lyase activity / L-cysteine desulfhydrase activity / transsulfuration / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
L-methionine gamma-lyase / : / Cys/Met metabolism enzymes pyridoxal-phosphate attachment site. / Cys/Met metabolism, pyridoxal phosphate-dependent enzyme / Cys/Met metabolism PLP-dependent enzyme / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
NITRATE ION / L-methionine gamma-lyase
Similarity search - Component
Biological speciesFusobacterium nucleatum subsp. nucleatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 Å
AuthorsKezuka, Y. / Yoshida, Y. / Nonaka, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP25462897 Japan
Japan Society for the Promotion of Science (JSPS)JP23792130 Japan
CitationJournal: To Be Published
Title: Crystal structure of methionine gamma-lyase from Fusobacterium nucleatum
Authors: Kezuka, Y.
History
DepositionFeb 12, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-methionine gamma-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1104
Polymers43,8681
Non-polymers2423
Water5,459303
1
A: L-methionine gamma-lyase
hetero molecules

A: L-methionine gamma-lyase
hetero molecules

A: L-methionine gamma-lyase
hetero molecules

A: L-methionine gamma-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,44116
Polymers175,4734
Non-polymers96912
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 area23690 Å2
ΔGint-157 kcal/mol
Surface area45970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.947, 99.915, 138.297
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-844-

HOH

21A-849-

HOH

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Components

#1: Protein L-methionine gamma-lyase / MGL / Homocysteine desulfhydrase / L-cysteine desulfidase


Mass: 43868.152 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusobacterium nucleatum subsp. nucleatum (strain ATCC 25586 / CIP 101130 / JCM 8532 / LMG 13131) (bacteria)
Gene: FN1419 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8RDT4, methionine gamma-lyase, homocysteine desulfhydrase, L-cysteine desulfidase
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.6 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 41% (v/v) 2-methyl-2,4-pentanediol (MPD), 0.2M Ammonium nitrate

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.19→43.06 Å / Num. obs: 145156 / % possible obs: 99.7 % / Redundancy: 13.5 % / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.017 / Rrim(I) all: 0.064 / Net I/σ(I): 26.3
Reflection shellResolution: 1.19→1.22 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 6.7 / Num. unique obs: 10334 / Rpim(I) all: 0.097 / Rrim(I) all: 0.285 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
DIALSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RFV

2rfv


Resolution: 1.19→37.78 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.405 / SU ML: 0.019 / Cross valid method: THROUGHOUT / ESU R: 0.031 / ESU R Free: 0.031 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16101 7273 5 %RANDOM
Rwork0.15198 ---
obs0.15243 137866 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 10.703 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20 Å20 Å2
2---0.03 Å20 Å2
3----0.51 Å2
Refinement stepCycle: 1 / Resolution: 1.19→37.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3022 0 16 303 3341
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193204
X-RAY DIFFRACTIONr_bond_other_d0.0020.023082
X-RAY DIFFRACTIONr_angle_refined_deg1.4191.9434358
X-RAY DIFFRACTIONr_angle_other_deg0.9082.9927175
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0445422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.64224.806129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.43815588
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0871514
X-RAY DIFFRACTIONr_chiral_restr0.0830.2512
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023536
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02600
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_it0.6380.951602
X-RAY DIFFRACTIONr_mcbond_other0.6370.9491601
X-RAY DIFFRACTIONr_mcangle_it1.0681.4262010
X-RAY DIFFRACTIONr_mcangle_other1.0691.4272011
X-RAY DIFFRACTIONr_scbond_it0.9321.0921601
X-RAY DIFFRACTIONr_scbond_other0.9311.0851596
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.4971.5782328
X-RAY DIFFRACTIONr_long_range_B_refined3.09812.1373632
X-RAY DIFFRACTIONr_long_range_B_other2.92211.7593568
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.19→1.221 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.208 538 -
Rwork0.197 9785 -
obs--96.46 %

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