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- PDB-9gj9: Crystal structure of methionine gamma-lyase from Brevibacterium s... -

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Basic information

Entry
Database: PDB / ID: 9gj9
TitleCrystal structure of methionine gamma-lyase from Brevibacterium sandarakinum in complex with PLP and norleucine at pH 6.5
ComponentsCystathionine gamma-synthase
KeywordsLYASE / Complex / inhibitor / methionine / PLP
Function / homology
Function and homology information


homocysteine desulfhydrase / methionine gamma-lyase / 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
NORLEUCINE / L-methionine gamma-lyase
Similarity search - Component
Biological speciesBrevibacterium sandarakinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.492 Å
AuthorsKopecny, D. / Ferchaud, N. / Briozzo, P.
Funding support Czech Republic, France, 4items
OrganizationGrant numberCountry
Ministry of Education, Youth and Sports of the Czech Republic8J23FR011 MOBILITY Czech Republic
Other governmentFR 49271QH BARRANDE France
Other privateIMEBATRACA France
Agence Nationale de la Recherche (ANR)ANR-11-IDEX-0003, Jean d'Alembert fellowship 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. / Simonson, T. / Machover, D. / Kopecny, D. / Briozzo, P.
History
DepositionAug 21, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)259,57712
Polymers258,7896
Non-polymers7876
Water93752
1
A: Cystathionine gamma-synthase
B: Cystathionine gamma-synthase
C: Cystathionine gamma-synthase
D: Cystathionine gamma-synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,0518
Polymers172,5264
Non-polymers5254
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19050 Å2
ΔGint-127 kcal/mol
Surface area46000 Å2
MethodPISA
2
E: Cystathionine gamma-synthase
F: Cystathionine gamma-synthase
hetero molecules

E: Cystathionine gamma-synthase
F: Cystathionine gamma-synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,0518
Polymers172,5264
Non-polymers5254
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area18920 Å2
ΔGint-125 kcal/mol
Surface area46390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.574, 229.734, 155.174
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 43131.578 Da / Num. of mol.: 6 / Mutation: None
Source method: isolated from a genetically manipulated source
Details: N-terminal His-tag / Source: (gene. exp.) Brevibacterium sandarakinum (bacteria) / Gene: SAMN04489751_4033 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1H1YBL2, methionine gamma-lyase
#2: Chemical
ChemComp-NLE / NORLEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H13NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.3 Å3/Da / Density % sol: 46.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Modified Morpheus I condition 2-4: 0.1 M Ethylene glycols, 0.08 M MES/Imidazole pH 6.5, 30% MPD, 10% PEG 1000, 10% PEG3350 and 5 mM Norleucine with 1 mM PLP Protein in starting drop: 7.4 mg ...Details: Modified Morpheus I condition 2-4: 0.1 M Ethylene glycols, 0.08 M MES/Imidazole pH 6.5, 30% MPD, 10% PEG 1000, 10% PEG3350 and 5 mM Norleucine with 1 mM PLP Protein in starting drop: 7.4 mg ml-1 in 50 mM HEPES, pH 7.5, 100 mM NaCl, 0.5 mM TCEP, 1 mM PLP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978565 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 2.492→114.867 Å / Num. obs: 34324 / % possible obs: 89.3 % / Redundancy: 6.66 %
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: 0.983 / CC1/2 anomalous: -0.004 / Rmerge(I) obs: 0.3252 / Rpim(I) all: 0.1319 / Rrim(I) all: 0.352 / AbsDiff over sigma anomalous: 0.642 / Baniso tensor eigenvalue 1: 30.1 Å2 / Baniso tensor eigenvalue 2: 40.9 Å2 / Baniso tensor eigenvalue 3: 162.2 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: 2.492 Å / Aniso diffraction limit 2: 2.902 Å / Aniso diffraction limit 3: 4.693 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): 4.27 / Num. measured all: 228757 / Orthogonalization convention: pdb / % possible anomalous: 88.8 / % possible ellipsoidal: 89.3 / % possible ellipsoidal anomalous: 88.8 / % possible spherical: 41.5 / % possible spherical anomalous: 40.3 / Redundancy anomalous: 3.5
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
8.47-114.8676.810.09829.671544515445226822680.994-0.0770.03870.1060.59399.499.299.499.299.43.8399.2
6.679-8.476.670.14197.221449814498217421740.991-0.0660.05630.15330.62195.396.895.396.895.33.6196.8
5.837-6.6797.380.26615.281454814548197119710.977-0.0140.1030.28630.64690.490.590.490.590.43.8990.5
5.306-5.8377.720.29465.121474414744191119110.979-0.0380.11110.31570.65588.58888.58888.54.0488
4.93-5.3067.910.33674.921467214672185418540.977-0.0670.12620.36040.648786.38786.3874.1286.3
4.645-4.938.020.30825.391441414414179717970.9830.0030.1150.32970.65786.185.486.185.185.84.1685.4
4.411-4.64580.3554.921422714227177917790.9850.0090.13350.38020.65188.788.788.783.484.14.1488.7
4.224-4.4117.890.34514.951353813538171617160.9810.0960.12950.36930.65293.493.493.481.682.24.0993.4
4.059-4.2247.130.4363.961210812108169816980.9770.0450.17470.47070.65895.495.595.478.5793.7195.5
3.918-4.0597.380.49813.751179311793159715970.963-0.0280.19540.53610.6796.99796.974.975.33.8297
3.793-3.9186.910.4993.751065610656154315430.943-0.020.2030.53990.65897.297.597.271.271.23.5897.5
3.678-3.7936.710.54033.431018510185151915190.939-0.0390.22570.58710.64298.29898.266.566.83.4798
3.571-3.6786.660.62442.991005010050151015100.93-0.0170.25860.67740.63897.998.197.96363.13.4598.1
3.466-3.5716.380.58623.0895969596150415040.9340.0260.24880.63840.6596.296.796.257.657.23.3196.7
3.361-3.4666.110.65652.7292729272151815180.9130.0160.28370.71690.6293.894.293.850.950.43.1794.2
3.254-3.3615.720.75932.2887518751152915290.883-0.0370.34120.83490.63890.691.790.645.244.42.9991.7
3.141-3.2545.210.61082.4180738073154915490.880.0330.28980.67810.64783.884.883.837.536.62.7284.8
3.013-3.1414.760.72391.9276147614159915990.8230.0220.36160.81210.65977.478.577.429.228.32.4978.5
2.862-3.0134.540.79381.6474357435163716370.7930.0010.40740.89590.61973.975.673.921.1202.3975.6
2.492-2.8624.320.78051.5671387138165116510.707-0.0090.41110.88720.63562.665.262.65.95.32.3265.2

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Processing

Software
NameVersionClassification
MxCuBEdata collection
autoPROCdata processing
autoPROCdata reduction
Aimless0.7.4data scaling
STARANISO2.3.63data scaling
PHASERphasing
BUSTER2.10.4refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.492→114.867 Å / Cor.coef. Fo:Fc: 0.88 / Cor.coef. Fo:Fc free: 0.844 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.651
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1706 -RANDOM
Rwork0.2552 ---
obs0.2568 34324 41.5 %-
Displacement parametersBiso mean: 56.19 Å2
Baniso -1Baniso -2Baniso -3
1--1.3191 Å20 Å20 Å2
2---2.3053 Å20 Å2
3---3.6244 Å2
Refine analyzeLuzzati coordinate error obs: 0.48 Å
Refinement stepCycle: LAST / Resolution: 2.492→114.867 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16803 0 144 52 16999
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00517268HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.7223588HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5605SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes2989HARMONIC5
X-RAY DIFFRACTIONt_it17268HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion2331SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact12767SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion1.84
X-RAY DIFFRACTIONt_other_torsion18.15
LS refinement shellResolution: 2.492→2.73 Å
RfactorNum. reflection% reflection
Rfree0.2988 39 -
Rwork0.33 --
obs--3.53 %
Refinement TLS params.

Method: refined / 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)
11.90640.53940.2741.8093-0.00811.6796-0.0718-0.2318-0.2118-0.2318-0.02920.2549-0.21180.25490.101-0.27450.00130.002-0.2692-0.02790.1633-20.0208-41.0253-15.8156
21.57330.09930.17881.67870.00631.4945-0.036-0.43030.3322-0.43030.0651-0.07060.3322-0.0706-0.0291-0.12510.01870.0306-0.0820.02250.5121-36.438-73.2233-16.9411
32.10080.1002-0.4321.99880.26521.77940.05020.10890.29980.10890.0069-0.08050.2998-0.0805-0.0571-0.32370.0211-0.067-0.22690.03790.1939-38.4026-73.151215.5547
41.94620.2185-0.00551.3290.19121.45930.09280.2626-0.20780.2626-0.09030.1488-0.20780.1488-0.0025-0.05950.080.0374-0.0163-0.02970.4317-18.7557-42.781716.6155
52.3271-0.62450.58812.04790.02061.7191-0.1114-0.3442-0.0655-0.34420.10420.4059-0.06550.40590.0072-0.2227-0.08850.0432-0.3138-0.03920.1879-43.51840.4224-16.1681
61.9527-0.0753-0.11851.31030.61371.9686-0.0499-0.292-0.1724-0.292-0.072-0.4215-0.1724-0.42150.1219-0.2451-0.0016-0.0712-0.33120.10430.2285-79.5419-0.8446-16.1366
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|389 }A1 - 389
2X-RAY DIFFRACTION1{ A|209 - A|401 }A209 - 401
3X-RAY DIFFRACTION1{ A|501 - A|520 }A501 - 520
4X-RAY DIFFRACTION2{ B|2 - B|389 }B2 - 389
5X-RAY DIFFRACTION2{ B|209 - B|401 }B209 - 401
6X-RAY DIFFRACTION2{ B|501 - B|507 }B501 - 507
7X-RAY DIFFRACTION3{ C|2 - C|389 }C2 - 389
8X-RAY DIFFRACTION3{ C|209 - C|401 }C209 - 401
9X-RAY DIFFRACTION3{ C|501 - C|506 }C501 - 506
10X-RAY DIFFRACTION4{ D|1 - D|389 }D1 - 389
11X-RAY DIFFRACTION4{ D|209 - D|401 }D209 - 401
12X-RAY DIFFRACTION4{ D|501 - D|508 }D501 - 508
13X-RAY DIFFRACTION5{ E|2 - E|389 }E2 - 389
14X-RAY DIFFRACTION5{ E|209 - E|401 }E209 - 401
15X-RAY DIFFRACTION5{ E|501 - E|507 }E501 - 507
16X-RAY DIFFRACTION6{ F|4 - F|389 }F4 - 389
17X-RAY DIFFRACTION6{ F|209 - F|401 }F209 - 401
18X-RAY DIFFRACTION6{ F|501 - F|504 }F501 - 504

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