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- PDB-9fyi: [4Fe-4S] Cluster-Containing L-Cysteine Desulfidase CyuA from Meth... -

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Basic information

Entry
Database: PDB / ID: 9fyi
Title[4Fe-4S] Cluster-Containing L-Cysteine Desulfidase CyuA from Methanococcus maripaludis
ComponentsL-cysteine desulfidase
KeywordsTRANSFERASE / CYSTEINE / CYSTEINE DESULFIDASE / DESULFURATION / SULFUR METABOLISM / SULFIDE / SULFUR TRANSFERASE / [FE-S] CLUSTER / IRON-SULFUR CLUSTER / [4Fe-4S] CLUSTER / LYASE
Function / homology
Function and homology information


L-cysteine desulfidase / : / 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
IRON/SULFUR CLUSTER / L-cysteine desulfidase
Similarity search - Component
Biological speciesMethanococcus maripaludis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.937 Å
AuthorsZecchin, P. / Pecqueur, L. / Golinelli, 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: Zecchin, P. / Golinelli, B.
History
DepositionJul 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 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)88,6756
Polymers87,7802
Non-polymers8954
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, The SEC-MALS analysis of apo-CyuA shows a main peak corresponding to a molar mass of 80.8 kDa, indicating a dimer (theoretical mass of monomer: 43.7 kDa).
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-106 kcal/mol
Surface area29340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.121, 79.148, 156.38
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 (archaea) / Gene: MMP1468 / Plasmid: PET15B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6LX84, L-cysteine desulfidase
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.37 Å3/Da / Density % sol: 48.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: ANAEROBY (<1.5 ppm O2) 13 % PEG 4000, 0.1 M NaCl, 0.1 M tri-sodium citrate dihydrate pH 5.5, 0.1 M LiSO4, 10 % glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980112 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980112 Å / Relative weight: 1
ReflectionResolution: 2.937→78.123 Å / Num. obs: 15210 / % possible obs: 92.78 % / Redundancy: 10.91 % / CC1/2: 0.9956 / Rrim(I) all: 0.119 / Net I/σ(I): 11.519
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
8.886-78.12310.3128.7867480.99120.062100
6.965-8.88511.2527.3137490.99830.072100
6.044-6.96510.8921.7787480.99810.092100
5.479-6.04311.819.9337490.99710.105100
5.072-5.47812.0118.6524780.99730.11100
4.759-5.07212.2419.5647490.99810.11100
4.513-4.57911.8618.3987480.99660.117100
4.31-4.51311.215.5317490.9950.139100
4.14-4.3111.9713.2767480.99380.168100
3.99-4.13912.1510.8567490.99260.204100
3.965-3.98911.998.2147480.9880.267100
3.749-3.86510.866.8547480.97740.325100
3.651-3.7495.475.1747490.97090.425100
3.557-3.6519.944.0927480.94410.539100
3.475-3.5579.843.127490.89730.723100
3.4-3.4759.832.3497480.85210.972100
3.329-3.49.831.9527490.77291.234100
3.262-3.3289.851.87480.72811.36395.53
3.191-3.2629.651.4927490.61161.58683.69
2.946-3.19110.331.2487480.521.9743.02

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Processing

Software
NameVersionClassification
autoPROCdata processing
XDSdata reduction
Aimlessdata scaling
STARANISOdata scaling
PHASESphasing
BUSTER2.10.4refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.937→70.62 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.49
RfactorNum. reflection% reflectionSelection details
Rfree0.2614 723 -RANDOM
Rwork0.2219 ---
obs0.2239 15210 82.6 %-
Displacement parametersBiso mean: 121.64 Å2
Baniso -1Baniso -2Baniso -3
1-1.3892 Å20 Å20 Å2
2---0.9708 Å20 Å2
3----0.4184 Å2
Refine analyzeLuzzati coordinate error obs: 0.44 Å
Refinement stepCycle: LAST / Resolution: 2.937→70.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5614 0 26 1 5641
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0075717HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.897717HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2023SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes950HARMONIC5
X-RAY DIFFRACTIONt_it5717HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion782SEMIHARMONIC5
X-RAY DIFFRACTIONt_utility_distance8HARMONIC1
X-RAY DIFFRACTIONt_utility_angle8HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact4484SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.32
X-RAY DIFFRACTIONt_other_torsion17.48
LS refinement shellResolution: 2.94→3.11 Å
RfactorNum. reflection% reflection
Rfree0.2539 19 -
Rwork0.3001 --
obs0.2979 423 14.47 %
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)
14.28642.0012-0.89931.50350.12914.07340.1839-0.25680.1755-0.2568-0.340.54420.17550.54420.1561-0.06870.09920.1315-0.0169-0.1257-0.035969.8116-5.262884.3768
24.2299-0.06320.4993.68560.87763.1481-0.13770.02980.08690.02980.23140.28640.08690.2864-0.0937-0.0797-0.1072-0.0055-0.1011-0.014-0.066246.8736-3.819998.8209
31.66861.6492.89772.8811-1.25054.5403-0.24170.06270.08760.06270.3025-0.54420.0876-0.5442-0.0608-0.0230.0769-0.11420.0774-0.1297-0.140825.21535.466898.4084
46.3926-0.7885-1.16185.20050.28641.0267-0.30520.44460.060.44460.239-0.08310.06-0.08310.0662-0.04720.114-0.1373-0.1903-0.1520.004448.73924.7026110.824
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|1 - 150}A1 - 150
2X-RAY DIFFRACTION2{A|153 - 401}A153 - 380
3X-RAY DIFFRACTION2{A|153 - 401}A401
4X-RAY DIFFRACTION3{B|4 - 150}B4 - 150
5X-RAY DIFFRACTION4{B|159 - 401}B159 - 377
6X-RAY DIFFRACTION4{B|159 - 401}B401

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