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- PDB-9he2: Crystal structure of CyuA C289A mutant from Methanococcus maripal... -

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Basic information

Entry
Database: PDB / ID: 9he2
TitleCrystal structure of CyuA C289A mutant from Methanococcus maripaludis with [4Fe-4S] clusters in complex with ethylene glycol
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: 3.74 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)88,5436
Polymers87,7152
Non-polymers8274
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, SEC-MALS analysis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-74 kcal/mol
Surface area30460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.632, 74.632, 251.059
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 156 through 393 or resid 401 through 402))
d_2ens_1(chain "B" and (resid 1 through 45 or resid 48...

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_12ASNASNLYSLYSAA156 - 393158 - 395
d_13SF4SF4SF4SF4AC401
d_14EDOEDOEDOEDOAD402
d_21METMETGLUGLUBB1 - 453 - 47
d_22GLUGLUVALVALBB48 - 12150 - 123
d_23ILEILEASNASNBB123 - 149125 - 151
d_24ASNASNLYSLYSBB156 - 393158 - 395
d_25SF4SF4SF4SF4BE401
d_26EDOEDOEDOEDOBF402

NCS oper: (Code: givenMatrix: (-0.995241737789, -0.0610507340476, -0.0759387334308), (0.0929684020888, -0.828296125936, -0.552523668246), (-0.0291677831841, -0.556954518458, 0.830030664971)Vector: 19. ...NCS oper: (Code: given
Matrix: (-0.995241737789, -0.0610507340476, -0.0759387334308), (0.0929684020888, -0.828296125936, -0.552523668246), (-0.0291677831841, -0.556954518458, 0.830030664971)
Vector: 19.8920473557, -35.2942752164, -10.2180384665)

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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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#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 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: 2.27 Å3/Da / Density % sol: 46.55 %
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: 3.738→19.905 Å / Num. obs: 7395 / % possible obs: 92.1 % / Redundancy: 10.95 %
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: 0.141 / Rmerge(I) obs: 0.1451 / Rpim(I) all: 0.0461 / Rrim(I) all: 0.1524 / AbsDiff over sigma anomalous: 0.788 / Baniso tensor eigenvalue 1: 51.491 Å2 / Baniso tensor eigenvalue 2: 51.491 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: 3.948 Å / Aniso diffraction limit 2: 3.948 Å / Aniso diffraction limit 3: 3.725 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): 8.95 / Num. measured all: 80984 / Observed signal threshold: 1.2 / Orthogonalization convention: pdb / % possible anomalous: 91.7 / % possible ellipsoidal: 92.1 / % possible ellipsoidal anomalous: 91.7 / % possible spherical: 83.1 / % possible spherical anomalous: 81.8 / Redundancy anomalous: 6.12 / 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
10.684-19.9059.50.047934.52351635163703700.9980.1350.01650.05081.2411001001001001005.98100
8.635-10.6369.660.061631.1357335733703700.9980.2860.02040.0651.1261001001001001005.7100
7.565-8.63210.770.076225.65397339733693690.9980.0550.0240.080.9711001001001001006.26100
6.88-7.561110.125815.72407040703703700.9960.1150.03930.1320.9281001001001001006.33100
6.385-6.8811.220.176712.48415141513703700.9930.1180.05410.18490.89199.699.799.699.799.66.3799.7
6.001-6.38411.580.248.99428442843703700.9910.1570.0730.25110.8391001001001001006.42100
5.691-6.00110.580.33696.4390339033693690.9780.1890.10680.35390.8931001001001001005.99100
5.443-5.6910.40.36325.88384738473703700.971-0.0270.11840.38250.7541001001001001005.71100
5.23-5.44310.120.43215.1374437443703700.964-0.0250.14260.45570.7449999.29999.2995.6899.2
5.046-5.2310.840.41565.22400940093703700.9780.010.13250.43660.75899.799.799.799.799.75.999.7
4.89-5.04610.960.43555.03404540453693690.971-0.1540.13650.45690.7341001001001001006.06100
4.745-4.88711.150.5094.42412741273703700.955-0.010.15880.53370.6831001001001001006.07100
4.614-4.74511.240.66013.52416041603703700.9460.1010.20430.69160.73899.799.599.799.599.76.1599.5
4.496-4.61411.260.69653.36416541653703700.962-0.050.21540.72970.6781001001001001006.17100
4.391-4.49611.570.84162.89427042703693690.9260.0350.25850.88140.7051001001001001006.27100
4.3-4.39111.521.11642.24426142613703700.822-0.0190.34151.16840.68699.799.799.799.799.76.2399.7
4.211-4.311.431.25651.93422942293703700.803-0.0790.38611.31560.6671001001001001006.26100
4.127-4.21111.781.34911.78435843583703700.8430.0390.40931.4110.6510099.510099.51006.3399.5
4.04-4.12711.861.62011.5437543753693690.8470.0460.48951.69360.6687.185.687.185.687.16.3185.6
3.738-4.03910.611.60391.34392439243703700.679-0.030.50841.68510.6737.139.337.120.518.66.0639.3

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Processing

Software
NameVersionClassification
autoPROC1.0.5data processing
XDSJun 30, 2024data reduction
STARANISO2.4.16data scaling
PHASERphasing
PHENIX1.21.2-5419refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.74→19.9 Å / SU ML: 0.3507 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 35.3379
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2627 382 5.17 %RANDOM
Rwork0.2171 7012 --
obs0.2197 7394 83.07 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 162.86 Å2
Refinement stepCycle: LAST / Resolution: 3.74→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5954 0 24 1 5979
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00286060
X-RAY DIFFRACTIONf_angle_d0.54768168
X-RAY DIFFRACTIONf_chiral_restr0.0391957
X-RAY DIFFRACTIONf_plane_restr0.00381025
X-RAY DIFFRACTIONf_dihedral_angle_d9.18152266
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.97323025502 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.74-4.270.2914540.32181314X-RAY DIFFRACTION47.58
4.27-5.370.33291420.28582804X-RAY DIFFRACTION100
5.37-19.90.23761860.17622894X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 10.090949457 Å / Origin y: -25.7477847522 Å / Origin z: 20.1543654176 Å
111213212223313233
T0.874222170183 Å2-0.0821238573519 Å2-0.104741103736 Å2-1.12817922279 Å20.127510897678 Å2--0.589236560493 Å2
L4.3054536621 °2-0.775143475279 °20.548996261251 °2-3.52792998697 °2-0.265759894881 °2--0.990458550944 °2
S-0.0714199235904 Å °0.243361826367 Å °0.484115934784 Å °-0.638938884833 Å °0.21077823023 Å °-0.0557074951355 Å °0.216060979211 Å °0.064379119561 Å °-0.122598732945 Å °
Refinement TLS groupSelection details: all

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