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- PDB-9hee: Crystal structure of methionine gamma-lyase from Brevibacterium a... -

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Basic information

Entry
Database: PDB / ID: 9hee
TitleCrystal structure of methionine gamma-lyase from Brevibacterium aurantiacum having disordered N-terminus and devoid of PLP cofactor
ComponentsCystathionine gamma-synthase
KeywordsLYASE / Apoform / methionine / PLP
Function / homology
Function and homology information


homocysteine desulfhydrase / methionine gamma-lyase / methionine gamma-lyase activity / cystathionine gamma-lyase activity / cysteine biosynthetic process via cystathionine / transsulfuration / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
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
L-methionine gamma-lyase
Similarity search - Component
Biological speciesBrevibacterium aurantiacum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.238 Å
AuthorsKopecny, D. / Ferchaud, N. / Briozzo, P.
Funding support Czech Republic, France, 4items
OrganizationGrant numberCountry
Ministry of Education, Youth and Sports of the Czech RepublicMOBILITY 8J23FR011 Czech Republic
Other governmentFR 49271QH PHC BARRANDE France
Other privateIMEBATRACA France
Agence Nationale de la Recherche (ANR)France 2023 ANR-11-IDEX-0003, Jean d'Alembert fellowship at Paris-Saclay France
CitationJournal: To Be Published
Title: Functional and structural characterization of methionine gamma-lyases from Brevibacterium bacteria: insights into cofactor retention
Authors: Ferchaud, N. / Boyer, A. / Odegard, B. / Hentati, S. / Machover, D. / Briozzo, P.
History
DepositionNov 13, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cystathionine gamma-synthase
B: Cystathionine gamma-synthase
C: Cystathionine gamma-synthase
D: Cystathionine gamma-synthase
E: Cystathionine gamma-synthase
F: Cystathionine gamma-synthase
G: Cystathionine gamma-synthase
H: Cystathionine gamma-synthase


Theoretical massNumber of molelcules
Total (without water)342,5648
Polymers342,5648
Non-polymers00
Water00
1
A: Cystathionine gamma-synthase
B: Cystathionine gamma-synthase
C: Cystathionine gamma-synthase
D: Cystathionine gamma-synthase


Theoretical massNumber of molelcules
Total (without water)171,2824
Polymers171,2824
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7140 Å2
ΔGint-54 kcal/mol
Surface area43600 Å2
MethodPISA
2
E: Cystathionine gamma-synthase
F: Cystathionine gamma-synthase
G: Cystathionine gamma-synthase
H: Cystathionine gamma-synthase


Theoretical massNumber of molelcules
Total (without water)171,2824
Polymers171,2824
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7050 Å2
ΔGint-53 kcal/mol
Surface area43940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.848, 165.848, 209.263
Angle α, β, γ (deg.)90, 90, 90
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
Cystathionine gamma-synthase / Methionine gamma-lyase (MGL)


Mass: 42820.480 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: N-terminal His-tag / Source: (gene. exp.) Brevibacterium aurantiacum (bacteria)
Gene: BAUR9175_03070, BAUR920_03040, BAURA63_02933, BAURA86_00394
Production host: Escherichia coli (E. coli) / Strain (production host): T7 express / References: UniProt: A0A2H1K3G9, methionine gamma-lyase
Has protein modificationN

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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: 2.22 Å3/Da / Density % sol: 41.44 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Well solution: 0.1 M MES pH 6.5, 0.6 M NaCl, 18% PEG4000, PLP 2 mM, Cryoprotection in glycerol 25%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 6, 2018 / Details: Kirkpatrick-Baez pair of bi-morph mirrors
RadiationMonochromator: channel cut cryogenically cooled monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3.237→129.978 Å / Num. obs: 30990 / % possible obs: 95.7 % / Redundancy: 20.01 %
Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last ...Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last updated 2020-04-13: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) and the actual quantities provided by MRFANA (https://github.com/githubgphl/MRFANA) from the autoPROC package (https://www.globalphasing.com/autoproc/). In general, the mmCIF categories here should provide items that are currently used in the PDB archive. If there are alternatives, the one recommended by the PDB developers has been selected. The distinction between *_all and *_obs quantities is not always clear: often only one version is actively used within the PDB archive (or is the one recommended by PDB developers). The intention of distinguishing between classes of reflections before and after some kind of observation criterion was applied, can in principle be useful - but such criteria change in various ways throughout the data processing steps (rejection of overloaded or too partial reflections, outlier/misfit rejections during scaling etc) and there is no retrospect computation of data scaling/merging statistics for the reflections used in the final refinement (where another observation criterion might have been applied). Typical data processing will usually only provide one version of statistics at various stages and these are given in the recommended item here, irrespective of the "_all" and "_obs" connotation, see e.g. the use of _reflns.pdbx_Rmerge_I_obs, _reflns.pdbx_Rrim_I_all and _reflns.pdbx_Rpim_I_all. Please note that all statistics related to "merged intensities" (or "merging") are based on inverse-variance weighting of the individual measurements making up a symmetry-unique reflection. This is standard for several decades now, even if some of the dictionary definitions seem to suggest that a simple "mean" or "average" intensity is being used instead. R-values are always given for all symmetry-equivalent reflections following Friedel's law, i.e. Bijvoet pairs are not treated separately (since we want to describe the overall mean intensity and not the mean I(+) and I(-) here). The Rrim metric is identical to the Rmeas R-value and only differs in name. _reflns.pdbx_number_measured_all is the number of measured intensities just before the final merging step (at which point no additional rejection takes place). _reflns.number_obs is the number of symmetry-unique observations, i.e. the result of merging those measurements via inverse-variance weighting. _reflns.pdbx_netI_over_sigmaI is based on the merged intensities (_reflns.number_obs) as expected. _reflns.pdbx_redundancy is synonymous with "multiplicity". The per-shell item _reflns_shell.number_measured_all corresponds to the overall value _reflns.pdbx_number_measured_all. The per-shell item _reflns_shell.number_unique_all corresponds to the overall value _reflns.number_obs. The per-shell item _reflns_shell.percent_possible_all corresponds to the overall value _reflns.percent_possible_obs. The per-shell item _reflns_shell.meanI_over_sigI_obs corresponds to the overall value given as _reflns.pdbx_netI_over_sigmaI. But be aware of the incorrect definition of the former in the current dictionary!
CC1/2: 0.999 / CC1/2 anomalous: -0.216 / Rmerge(I) obs: 0.1532 / Rpim(I) all: 0.0351 / Rrim(I) all: 0.1572 / AbsDiff over sigma anomalous: 0.691 / Baniso tensor eigenvalue 1: 74.5266 Å2 / Baniso tensor eigenvalue 2: 74.5266 Å2 / Baniso tensor eigenvalue 3: 0 Å2 / Baniso tensor eigenvector 1 ortho1: 1 / Baniso tensor eigenvector 1 ortho2: 0 / Baniso tensor eigenvector 1 ortho3: 0 / Baniso tensor eigenvector 2 ortho1: 0 / Baniso tensor eigenvector 2 ortho2: 1 / Baniso tensor eigenvector 2 ortho3: 0 / Baniso tensor eigenvector 3 ortho1: 0 / Baniso tensor eigenvector 3 ortho2: 0 / Baniso tensor eigenvector 3 ortho3: 1 / Aniso diffraction limit 1: 3.937 Å / Aniso diffraction limit 2: 3.937 Å / Aniso diffraction limit 3: 3.219 Å / Aniso diffraction limit axis 1 ortho1: 1 / Aniso diffraction limit axis 1 ortho2: 0 / Aniso diffraction limit axis 1 ortho3: 0 / Aniso diffraction limit axis 2 ortho1: 0 / Aniso diffraction limit axis 2 ortho2: 1 / Aniso diffraction limit axis 2 ortho3: 0 / Aniso diffraction limit axis 3 ortho1: 0 / Aniso diffraction limit axis 3 ortho2: 0 / Aniso diffraction limit axis 3 ortho3: 1 / Net I/σ(I): 13.06 / Num. measured all: 620053 / Observed signal threshold: 1.2 / Orthogonalization convention: pdb / % possible anomalous: 95.7 / % possible ellipsoidal: 95.7 / % possible ellipsoidal anomalous: 95.7 / % possible spherical: 65.7 / % possible spherical anomalous: 64.3 / Redundancy anomalous: 10.7 / Signal type: local
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsCC1/2CC1/2 anomalousRpim(I) allRrim(I) allAbsDiff over sigma anomalous% possible anomalous% possible ellipsoidal% possible ellipsoidal anomalous% possible spherical% possible spherical anomalousRedundancy anomalous% possible all
10.496-129.97816.880.05837.392616826168155015500.999-0.3190.01410.05970.53210010010010010010.09100
8.25-10.49519.40.064238.223005330053154915490.999-0.3440.01490.06590.55510010010010010010.81100
7.16-8.24919.130.085130.592964829648155015500.998-0.2750.01980.08740.6910010010010010010.43100
6.486-7.15920.030.119623.153103031030154915490.998-0.2040.02720.12270.71999.999.999.999.999.910.8599.9
6.003-6.48618.980.142619.212942629426155015500.996-0.2250.03330.14650.71110010010010010010.19100
5.638-6.00220.010.162116.63098830988154915490.997-0.120.03690.16630.73310010010010010010.73100
5.345-5.63820.560.189414.463186631866155015500.996-0.1340.04260.19420.69710010010010010010.95100
5.107-5.34420.80.225712.323221332213154915490.996-0.1410.05050.23140.70410010010010010011.07100
4.903-5.10720.040.264410.443106731067155015500.994-0.0840.06010.27120.68310010010010010010.61100
4.731-4.90219.580.27819.943033030330154915490.993-0.070.06410.28550.72510010010010010010.38100
4.579-4.7320.470.29899.73173431734155015500.992-0.0910.06730.30640.70310010010010010010.82100
4.444-4.57920.770.36388.273216832168154915490.989-0.0640.08130.37290.71999.999.999.999.999.910.9799.9
4.326-4.44419.680.41497.013050030500155015500.988-0.080.09550.42590.69610010010010010010.37100
4.216-4.32619.490.51445.673018630186154915490.983-0.0090.11890.52810.71110010010010010010.22100
4.119-4.21620.190.6934.433129431294155015500.974-0.0370.15720.71080.68810010010010010010.63100
4.027-4.11920.631.00663.283195531955154915490.9450.0020.22621.0320.69498.798.198.798.198.710.7998.1
3.925-4.02720.941.04083.273245532455155015500.941-0.0260.23211.06670.68682.481.482.48081.110.981.4
3.804-3.92520.911.22122.833238432384154915490.9070.0190.27251.25160.71589.188.889.160.460.910.988.8
3.628-3.80420.481.43562.433173731737155015500.985-0.0320.32441.47240.7058181.88135.334.510.8181.8
3.237-3.62821.211.91511.93285132851154915490.742-00.42331.96210.70676.977.376.911.510.611.4177.3

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Processing

Software
NameVersionClassification
autoPROC1.0.5 20240123data processing
XDSJun 30, 2023data reduction
Aimless0.7.15data scaling
STARANISO2.4.9data scaling
BUSTER2.10.4refinement
Coot0.9.8model building
PHASER2.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.238→32.76 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.882 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.791
RfactorNum. reflection% reflectionSelection details
Rfree0.2843 1518 -RANDOM
Rwork0.2469 ---
obs0.2487 30928 65.8 %-
Displacement parametersBiso mean: 163.93 Å2
Baniso -1Baniso -2Baniso -3
1-0.6572 Å20 Å20 Å2
2--0.6572 Å20 Å2
3----1.3144 Å2
Refine analyzeLuzzati coordinate error obs: 0.56 Å
Refinement stepCycle: LAST / Resolution: 3.238→32.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18176 0 0 0 18176
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00618504HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.7925240HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6056SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes3184HARMONIC5
X-RAY DIFFRACTIONt_it18504HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion2504SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact13811SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion1.87
X-RAY DIFFRACTIONt_other_torsion21.03
LS refinement shellResolution: 3.24→3.47 Å
RfactorNum. reflection% reflection
Rfree0.3187 32 -
Rwork0.3294 --
obs0.3289 619 7.1 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.9316-1.9548-0.31252.58820.0264.0257-0.03810.28550.92670.2855-0.1381-0.56950.9267-0.56950.17620.2985-0.20360.091-0.2045-0.1016-0.0256-15.658935.963-34.1064
22.3371-2.9678-0.17548.9329-2.95355.17890.09440.27580.24440.2758-0.41870.36760.24440.36760.3242-0.16160.0131-0.1095-0.0741-0.1967-0.13487.594941.3553-65.8471
33.5951-3.0199-0.57147.1186-0.41242.52670.1348-0.66960.3092-0.6696-0.32080.05180.30920.05180.186-0.1717-0.0096-0.03570.2047-0.0188-0.0815-18.201367.7284-78.2133
45.4635-2.75382.73135.0358-2.35646.6223-0.41190.7374-0.4250.73740.2937-0.7497-0.425-0.74970.1183-0.2110.01050.1859-0.0438-0.0275-0.0991-31.713771.2551-41.3582
58.8070.6031-1.54985.82511.19967.833-0.3815-0.16022.0617-0.1602-0.082-0.48722.0617-0.48720.46350.8743-0.07380.0157-0.8944-0.3095-0.564817.5803-4.73-82.9645
69.65632.3598-1.9314.05032.993910.520.109-0.0340.7195-0.0340.4441.62420.71951.6242-0.553-0.390.6080.03050.77730.1327-0.596849.061310.8795-100.77
77.74992.15921.03361.5498-0.72127.4647-0.56790.0751-0.23120.07510.13630.9237-0.23120.92370.4316-0.73180.269-0.2517-0.2565-0.08470.918253.375135.2672-70.3713
84.3012-0.2967-0.21036.83310.77813.177-0.47670.71980.66250.71980.33150.30140.66250.30140.14530.14460.608-0.16670.1326-0.1957-0.446731.72539.7728-49.1371
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A67 - 389
2X-RAY DIFFRACTION2{ B|* }B67 - 389
3X-RAY DIFFRACTION3{ C|* }C67 - 389
4X-RAY DIFFRACTION4{ D|* }D67 - 389
5X-RAY DIFFRACTION5{ E|* }E67 - 389
6X-RAY DIFFRACTION6{ F|* }F67 - 389
7X-RAY DIFFRACTION7{ G|* }G67 - 389
8X-RAY DIFFRACTION8{ H|* }H67 - 389

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