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- PDB-9gmc: Crystal structure of the complex formed between the radical SAM p... -

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Basic information

Entry
Database: PDB / ID: 9gmc
TitleCrystal structure of the complex formed between the radical SAM protein ChlB and the R3A mutant of ChlA
Components
  • ChlA R3A mutant
  • ChlB radical SAM domain
KeywordsOXIDOREDUCTASE / Radical SAM protein Ribosomally synthesised and post-translationally modified peptides Iron sulfur clusters Peptide binding protein
Function / homologyACETATE ION / S-ADENOSYL-L-HOMOCYSTEINE / IRON/SULFUR CLUSTER
Function and homology information
Biological speciesFischerella (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
Authorsde la Mora, E. / Ruel, J. / Usclat, A. / Martin, L. / Amara, P. / Morinaka, B. / Nicolet, Y.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)SAM4RiPP France
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: Peptide Recognition and Mechanism of the Radical S -Adenosyl-l-methionine Multiple Cyclophane Synthase ChlB.
Authors: Ruel, J. / Nguyen, T.Q.N. / Morishita, Y. / Usclat, A. / Martin, L. / Amara, P. / Kieffer-Jaquinod, S. / Stefanoiu, M.C. / de la Mora, E. / Morinaka, B.I. / Nicolet, Y.
History
DepositionAug 28, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 25, 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: ChlB radical SAM domain
B: ChlA R3A mutant
C: ChlB radical SAM domain
D: ChlA R3A mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,48219
Polymers103,7764
Non-polymers2,70715
Water10,881604
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9470 Å2
ΔGint-139 kcal/mol
Surface area31400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.692, 62.467, 113.138
Angle α, β, γ (deg.)90, 117.33, 90
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein ChlB radical SAM domain


Mass: 41981.801 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fischerella (bacteria) / Production host: Escherichia coli (E. coli)
#2: Protein ChlA R3A mutant


Mass: 9906.050 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fischerella (bacteria) / Production host: Escherichia coli (E. coli)

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Non-polymers , 4 types, 619 molecules

#3: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 604 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.38 Å3/Da / Density % sol: 48.37 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 3.1 M sodium formate 0.1 M Tris p H 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.77→100.509 Å / Num. obs: 61496 / % possible obs: 92 % / Redundancy: 6.86 %
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: 0.996 / CC1/2 anomalous: -0.014 / Rmerge(I) obs: 0.1595 / Rpim(I) all: 0.0651 / Rrim(I) all: 0.1725 / AbsDiff over sigma anomalous: 0.686 / Baniso tensor eigenvalue 1: 2.1313 Å2 / Baniso tensor eigenvalue 2: 0 Å2 / Baniso tensor eigenvalue 3: 36.6059 Å2 / Baniso tensor eigenvector 1 ortho1: 0.9633 / Baniso tensor eigenvector 1 ortho2: 0 / Baniso tensor eigenvector 1 ortho3: 0.2683 / Baniso tensor eigenvector 2 ortho1: 0 / Baniso tensor eigenvector 2 ortho2: 1 / Baniso tensor eigenvector 2 ortho3: 0 / Baniso tensor eigenvector 3 ortho1: -0.2683 / Baniso tensor eigenvector 3 ortho2: 0 / Baniso tensor eigenvector 3 ortho3: 0.9633 / Aniso diffraction limit 1: 1.781 Å / Aniso diffraction limit 2: 1.769 Å / Aniso diffraction limit 3: 2.424 Å / Aniso diffraction limit axis 1 ortho1: 0.97332 / Aniso diffraction limit axis 1 ortho2: 0 / Aniso diffraction limit axis 1 ortho3: 0.22928 / 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: -0.22928 / Aniso diffraction limit axis 3 ortho2: 0 / Aniso diffraction limit axis 3 ortho3: 0.97332 / Net I/σ(I): 5.41 / Num. measured all: 422011 / Observed signal threshold: 1.2 / Orthogonalization convention: pdb / % possible anomalous: 91.7 / % possible ellipsoidal: 92 / % possible ellipsoidal anomalous: 91.7 / % possible spherical: 66.9 / % possible spherical anomalous: 66.7 / Redundancy anomalous: 3.51 / 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
5.576-100.5096.890.055611.452119821198307530750.9970.1970.02290.06020.52999.710099.710099.73.68100
4.408-5.5767.190.061911.322209722097307530750.997-0.1120.02480.06670.43999.910099.910099.93.73100
3.839-4.4087.250.069411.092227522275307430740.996-0.1340.02770.07480.4591001001001001003.74100
3.484-3.8397.210.085710.032218322183307530750.995-0.1330.03430.09230.52699.910099.910099.93.71100
3.21-3.4835.950.10818.081828318283307530750.991-0.0810.04820.11870.60990.391.190.391.190.33.0691.1
3.018-3.216.290.14247.091934819348307530750.989-0.0160.06140.15550.64797.598.597.598.597.53.2498.5
2.867-3.0186.60.19166.212029120291307530750.9820.0170.08010.2080.6998.599.198.599.198.53.3899.1
2.742-2.8676.710.23815.442061620616307430740.977-0.0020.09890.25820.70399.599.599.599.599.53.4299.5
2.636-2.7426.830.29334.782099120991307530750.970.0170.12020.31740.71999.899.799.899.799.83.4899.7
2.546-2.6366.860.3714.082109221092307530750.961-0.050.15130.40120.73699.999.799.999.799.93.4999.7
2.464-2.5466.910.40683.862125621256307530750.95-0.0120.16550.43970.72698.197.798.197.798.13.5197.7
2.39-2.4646.960.45663.692139621396307530750.937-0.0110.18480.49310.75294.694.194.693.393.93.5394.1
2.317-2.396.960.46583.632139321393307430740.936-0.0020.18870.50310.75692.292.192.285.786.43.5392.1
2.249-2.31770.51153.482153321533307530750.917-0.0460.20620.55210.74192.392.492.380.180.73.5592.4
2.184-2.2497.010.61213.12156121561307530750.9010.010.24620.66050.76593.193.393.174.5753.5593.3
2.12-2.1847.010.70732.82157121571307530750.871-0.0170.28420.7630.77792.993.292.968.869.33.5693.2
2.058-2.1270.84392.512151521515307530750.813-0.0270.34020.91090.7629292.39261.6623.5492.3
1.995-2.0587.031.04892.152161421614307430740.742-0.0160.42091.13130.77490.590.890.554.154.53.5690.8
1.924-1.9957.11.30841.842182521825307530750.6380.0380.52351.41070.78283.683.883.641.942.23.683.8
1.77-1.9246.51.51071.511997319973307530750.528-0.0130.63151.64040.78754.454.854.415.215.23.354.8

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Processing

Software
NameVersionClassification
autoPROC1.0.5 20230726data processing
XDSJun 30, 2023data reduction
Aimless0.7.13data scaling
STARANISO2.3.94data scaling
BUSTER2.10.4refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→100.51 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.936 / SU R Cruickshank DPI: 0.17 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.177 / SU Rfree Blow DPI: 0.15 / SU Rfree Cruickshank DPI: 0.149
RfactorNum. reflection% reflectionSelection details
Rfree0.214 3120 -RANDOM
Rwork0.1777 ---
obs0.1795 61496 67 %-
Displacement parametersBiso mean: 28.45 Å2
Baniso -1Baniso -2Baniso -3
1-0.4023 Å20 Å2-0.3301 Å2
2---0.1449 Å20 Å2
3----0.2574 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 1.77→100.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6368 0 120 604 7092
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0096879HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.969432HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2414SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1222HARMONIC5
X-RAY DIFFRACTIONt_it6879HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion912SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact6473SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.28
X-RAY DIFFRACTIONt_other_torsion16.86
LS refinement shellResolution: 1.77→1.87 Å
RfactorNum. reflection% reflection
Rfree0.3064 62 -
Rwork0.2695 --
obs0.2712 1230 8.84 %
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)
10.49950.1340.22210.23370.14220.3783-0.0136-0.0028-0.0065-0.00280.0291-0.0052-0.0065-0.0052-0.0155-0.05760.0015-0.005-0.0402-0.00370.0302-23.7182-31.00824.5384
22.2268-1.48850.88260.2003-0.2380.9626-0.02270.04070.10360.0407-0.11660.1790.10360.1790.1393-0.08980.01830.00360.02090.04070.0231.5724-31.697713.0989
30.1894-0.00450.09160.5831-0.32930.39960.0336-0.06690.0543-0.06690.0269-0.01170.0543-0.0117-0.06050.01550.0032-0.0302-0.04630.0074-0.03223.5505-60.466637.6816
44.32240.7652-0.90661.9341.57323.444-0.16340.02790.32640.02790.0904-0.16520.3264-0.16520.0729-0.0112-0.059-0.1717-0.1654-0.03060.0143-9.5224-59.888814.8239
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|3 - A|375 }A3 - 375
2X-RAY DIFFRACTION2{ B|19 - B|53 }B19 - 53
3X-RAY DIFFRACTION3{ C|3 - C|374 }C3 - 374
4X-RAY DIFFRACTION4{ D|20 - D|48 }D20 - 48

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