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- PDB-9fsl: Crystal structure of CyuA from Methanococcus maripaludis with [2F... -

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Basic information

Entry
Database: PDB / ID: 9fsl
TitleCrystal structure of CyuA from Methanococcus maripaludis with [2Fe-2S] clusters solved by Fe-SAD
ComponentsL-cysteine desulfidase
KeywordsLYASE / L-cysteine desulfidase / iron-sulfur cluster / cysteine / sulfur metabolism / sulfide
Function / homology
Function and homology information


L-cysteine desulfidase / L-cysteine catabolic process to pyruvate / L-cysteine desulfhydrase activity / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
Uncharacterised protein family UPF0597 / Serine dehydratase-like, alpha subunit / Serine dehydratase alpha chain
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / L-cysteine desulfidase
Similarity search - Component
Biological speciesMethanococcus maripaludis S2 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.417 Å
AuthorsPecqueur, L. / He, N. / Golinelli-Pimpaneau, B.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-11-LABX-0011 France
CitationJournal: To Be Published
Title: Insights into the phylogenetic distribution, structure and function of [4Fe-4S]-dependent L-cysteine desulfidase, an enzyme that supplies sulfide to the archaeon Methanococcus maripaludis
Authors: Golinelli-Pimpaneau, B.
History
DepositionJun 21, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 2, 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: L-cysteine desulfidase
B: L-cysteine desulfidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,3626
Polymers87,7802
Non-polymers5824
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-61 kcal/mol
Surface area29960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.166, 77.226, 153.969
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein L-cysteine desulfidase / L-cysteine desulfhydrase


Mass: 43889.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanococcus maripaludis S2 (archaea) / Gene: MMP1468 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6LX84, L-cysteine desulfidase
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.17 Å3/Da / Density % sol: 39 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: ANAEROBY (<1.5 ppm O2) 14% w/v PEG 4K 0.1M Mes pH 6.5 O.1M NaCl 0.1M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 1.7389 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7389 Å / Relative weight: 1
ReflectionResolution: 2.417→76.985 Å / Num. obs: 23186 / % possible obs: 92.4 % / Redundancy: 23.3 %
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: 0.998 / CC1/2 anomalous: 0.352 / Rmerge(I) obs: 0.1114 / Rpim(I) all: 0.0233 / Rrim(I) all: 0.1139 / AbsDiff over sigma anomalous: 0.838 / Baniso tensor eigenvalue 1: 16.1531 Å2 / Baniso tensor eigenvalue 2: 40.5572 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: 2.528 Å / Aniso diffraction limit 2: 2.791 Å / Aniso diffraction limit 3: 2.407 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): 16.52 / Num. measured all: 540267 / Observed signal threshold: 1.2 / Orthogonalization convention: pdb / % possible anomalous: 91.1 / % possible ellipsoidal: 92.4 / % possible ellipsoidal anomalous: 91.1 / % possible spherical: 77.2 / % possible spherical anomalous: 75.4 / Redundancy anomalous: 12.56 / 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
7.431-76.98523.740.059443.362751427514115911590.9980.4530.01240.06082.40710010010010010014.15100
5.824-7.42923.320.075638.512705127051116011600.9980.3930.0160.07742.00810010010010010012.97100
5.057-5.82424.820.086336.742876528765115911590.9970.0740.01780.08821.53610010010010010013.51100
4.58-5.05722.940.083636.162659326593115911590.997-0.1760.01790.08551.02110010010010010012.37100
4.245-4.5824.740.090935.212869628696116011600.997-0.2980.01880.09280.91310010010010010013.34100
3.984-4.24525.270.10330.622929229292115911590.997-0.2420.02110.10520.79910010010010010013.51100
3.775-3.98421.280.128121.892465824658115911590.995-0.2720.02770.13130.76894.997.694.997.694.911.5997.6
3.589-3.77421.110.152118.72446224462115911590.993-0.2480.03250.15570.72686.989.886.989.886.911.5489.8
3.45-3.58822.340.198915.112591525915116011600.992-0.1950.04220.20360.71198.999.898.999.898.911.9899.8
3.317-3.4520.250.262710.782347523475115911590.991-0.1410.05680.26910.6285.189.885.189.885.111.2389.8
3.211-3.31725.10.3579.762909429094115911590.989-0.1840.07250.36440.62110010010010010013.17100
3.12-3.21125.110.43668.32913129131116011600.987-0.1130.08840.44560.58410010010010010013.3100
3.037-3.1225.270.61986.292929129291115911590.977-0.0640.12510.63250.59310010010010010013.33100
2.963-3.03723.180.85014.482686026860115911590.96700.17960.86910.58710010010010010012.2100
2.896-2.96323.671.0953.712745927459116011600.954-0.0540.22881.1190.5710010010010010012.45100
2.831-2.89624.631.40843.182854128541115911590.939-0.0210.28831.4380.58597.296.597.296.597.212.8896.5
2.767-2.83124.511.7542.642840428404115911590.9090.0110.35891.79080.55489.188.889.188.588.912.8388.8
2.701-2.76724.492.23182.232838728387115911590.886-0.0530.4572.27880.55186.68786.677.677.912.7987
2.622-2.70116.073.05231.291864018640116011600.3880.0360.72763.14770.55769.177.769.158.652.49.2977.7
2.417-2.62124.194.0691.482803928039115911590.750.0520.83984.15610.56755.555.755.518.217.612.8355.7

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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
PHASER2.8.2phasing
PARROT1.0.4phasing
CRANK22.0.281phasing
RefinementMethod to determine structure: SAD / Resolution: 2.417→76.98 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.915 / SU R Cruickshank DPI: 2.087 / Cross valid method: THROUGHOUT / SU R Blow DPI: 1.975 / SU Rfree Blow DPI: 0.352 / SU Rfree Cruickshank DPI: 0.358
RfactorNum. reflection% reflectionSelection details
Rfree0.2761 1118 -RANDOM
Rwork0.2319 ---
obs0.234 23186 77.2 %-
Displacement parametersBiso mean: 89.58 Å2
Baniso -1Baniso -2Baniso -3
1-2.5207 Å20 Å20 Å2
2--1.8103 Å20 Å2
3----4.331 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: LAST / Resolution: 2.417→76.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5619 0 21 19 5659
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0075729HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.927715HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2051SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes953HARMONIC5
X-RAY DIFFRACTIONt_it5729HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion784SEMIHARMONIC5
X-RAY DIFFRACTIONt_utility_distance8HARMONIC1
X-RAY DIFFRACTIONt_utility_angle8HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact4451SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.66
X-RAY DIFFRACTIONt_other_torsion18.01
LS refinement shellResolution: 2.42→2.56 Å
RfactorNum. reflection% reflection
Rfree0.2976 25 -
Rwork0.3034 --
obs0.3031 464 10.29 %
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)
14.73270.811-0.80082.67970.67934.74990.1068-0.04320.0222-0.0432-0.10690.81670.02220.81670.0001-0.1020.07560.037-0.0516-0.06470.004468.4708-4.481382.9672
26.3104-0.2384-0.37593.70110.88784.1426-0.22630.1520.12950.1520.1251-0.11330.1295-0.11330.1013-0.0284-0.06870.0353-0.1398-0.0026-0.155645.7114-2.748497.3474
33.2130.81031.96254.1912-1.00996.0625-0.1360.2630.2840.2630.1087-1.03170.284-1.03170.0274-0.0465-0.14240.02210.0892-0.1428-0.245924.413835.417297.0309
49.1667-1.8397-1.24075.50151.91735.6865-0.44790.68120.04120.68120.56710.18390.04120.1839-0.1193-0.04660.0525-0.1861-0.1626-0.2136-0.180746.976325.469108.458
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|1 - 146}A1 - 146
2X-RAY DIFFRACTION2{A|157 - 378}A157 - 378
3X-RAY DIFFRACTION3{B|2 - 146}B2 - 146
4X-RAY DIFFRACTION4{B|157 - 384}B157 - 384

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