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- PDB-9he0: Crystal structure of CyuA C289A mutant from Methanococcus maripal... -

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Basic information

Entry
Database: PDB / ID: 9he0
TitleCrystal structure of CyuA C289A mutant from Methanococcus maripaludis with [4Fe-4S] clusters in complex with glycerol
ComponentsL-cysteine desulfidase
KeywordsLYASE / L-cysteine desulfidase / iron-sulfur cluster / sulfur metabolism
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
IRON/SULFUR CLUSTER / L-cysteine desulfidase
Similarity search - Component
Biological speciesMethanococcus maripaludis S2 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.18 Å
AuthorsGervason, S. / Pecqueur, L. / Golinelli-Pimpaneau, B.
Funding support France, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-11-labx-0011 France
Agence Nationale de la Recherche (ANR)ANR-22-CE44-0012 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 archeon Methanococcus maripaludis
Authors: Golinelli-Pimpaneau, B.
History
DepositionNov 13, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 5, 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)88,6036
Polymers87,7152
Non-polymers8874
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, SEC-MALS analysis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-80 kcal/mol
Surface area29740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.694, 73.694, 251.349
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 149 or resid 154 through 402))
d_2ens_1(chain "B" and (resid 1 through 149 or resid 154 through 402))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11METMETASNASNAA1 - 1493 - 151
d_12GLUGLULYSLYSAA154 - 393156 - 395
d_13SF4SF4SF4SF4AC401
d_14GOLGOLGOLGOLAD402
d_21METMETASNASNBB1 - 1493 - 151
d_22GLUGLULYSLYSBB154 - 393156 - 395
d_23SF4SF4SF4SF4BE401
d_24GOLGOLGOLGOLBF402

NCS oper: (Code: givenMatrix: (-0.995431523731, -0.0679510511555, -0.0670726189226), (0.0934445357437, -0.837568029412, -0.538282374638), (-0.0196010280833, -0.54209081412, 0.840091274175)Vector: 19. ...NCS oper: (Code: given
Matrix: (-0.995431523731, -0.0679510511555, -0.0670726189226), (0.0934445357437, -0.837568029412, -0.538282374638), (-0.0196010280833, -0.54209081412, 0.840091274175)
Vector: 19.4081162478, -35.6137874709, -10.1358423632)

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Components

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


Mass: 43857.711 Da / Num. of mol.: 2 / Mutation: C289A
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-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
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: 2.21 Å3/Da / Density % sol: 45.24 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: ANAEROBY (<1.5 ppm O2) 12% w/v PEG 4000 0.1M tri-sodium citrate dihydrate pH 5.5 0.1M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 13, 2024
RadiationMonochromator: Si filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 3.18→19.9 Å / Num. obs: 11320 / % possible obs: 81.3 % / Redundancy: 19.6 % / Biso Wilson estimate: 110.96 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.449 / Rpim(I) all: 0.104 / Rrim(I) all: 0.461 / Net I/σ(I): 6.5
Reflection shell

Num. unique obs: 566 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Rpim(I) allRrim(I) all
9.297-19.90.10820.8370.99680.0270.111
7.447-9.2890.13318.6220.99550.0310.136
6.514-7.4440.21612.4820.99360.0490.222
5.919-6.5140.3249.1840.98550.0730.333
5.489-5.9180.4276.8370.9820.1020.439
5.16-5.4880.4227.160.9770.10.434
4.886-5.1560.4277.5720.97080.0980.438
4.673-4.8860.4447.4420.97630.1010.455
4.49-4.6730.5256.6080.97160.1190.538
4.328-4.490.6365.7920.97410.1440.652
4.195-4.3280.725.0630.94850.1620.738
4.067-4.1950.9314.1730.94070.2080.955
3.961-4.0670.94381.1783.4710.2641.208
3.859-3.9611.3633.0620.8870.3151.4
3.77-3.8591.6542.5520.83740.3781.697
3.686-3.771.8052.3540.8050.4351.858
3.614-3.6862.411.90.69260.5552.474
3.532-3.6142.9061.6940.6860.6632.982
3.423-3.5323.3151.5460.59930.7613.403
3.184-3.4224.3831.3240.5030.9974.496

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Processing

Software
NameVersionClassification
autoPROC1.0.5data processing
XDSJun 30, 2023data reduction
STARANISO2.4.9data scaling
PHASERphasing
PHENIX1.21.2-5419refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.18→19.9 Å / SU ML: 0.4653 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.7535
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.239 562 4.96 %RANDOM
Rwork0.2095 10758 --
obs0.2111 11320 81.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.64 Å2
Refinement stepCycle: LAST / Resolution: 3.18→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6005 0 28 0 6033
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00216117
X-RAY DIFFRACTIONf_angle_d0.48628247
X-RAY DIFFRACTIONf_chiral_restr0.04966
X-RAY DIFFRACTIONf_plane_restr0.00341034
X-RAY DIFFRACTIONf_dihedral_angle_d9.16692293
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.03960591788 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.18-3.50.319490.3061916X-RAY DIFFRACTION28.37
3.5-4.010.29681350.26023111X-RAY DIFFRACTION95.05
4.01-5.030.24281620.20323311X-RAY DIFFRACTION100
5.04-19.90.21412160.18333420X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 9.9421126938 Å / Origin y: -25.561305498 Å / Origin z: 20.176464727 Å
111213212223313233
T0.490947853948 Å20.0597414544084 Å20.015149378946 Å2-0.627857105251 Å20.0319412628155 Å2--0.440809996756 Å2
L1.90495153273 °2-0.200842245312 °20.505205463262 °2-1.28734305156 °2-0.0796414680649 °2--1.08423634074 °2
S0.148880044548 Å °0.0430766848338 Å °0.0677052047851 Å °-0.097819385973 Å °-0.0604645079382 Å °-0.0358856702398 Å °0.0478875403739 Å °0.0835314539155 Å °-0.0956053551234 Å °
Refinement TLS groupSelection details: all

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