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- PDB-9n1c: Crystal structure of CysS from Corallococcus sp. CA054B with 5'-d... -

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Basic information

Entry
Database: PDB / ID: 9n1c
TitleCrystal structure of CysS from Corallococcus sp. CA054B with 5'-deoxyadenosine, methionine, and pantetheinylated 3-ethoxy-4-amino benzoic acid substrate bound
ComponentsRadical SAM enzyme CysS
KeywordsOXIDOREDUCTASE/SUBSTRATE / cystobactamids / radical S-adenosylmethionine methylase / cobalamin / OXIDOREDUCTASE / OXIDOREDUCTASE-SUBSTRATE complex
Function / homology5'-DEOXYADENOSINE / : / COBALAMIN / METHIONINE / IRON/SULFUR CLUSTER / :
Function and homology information
Biological speciesCorallococcus sp. CA054B (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWang, B. / Cui, J. / Booker, S.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-122595 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2026
Title: Structural basis for iterative methylation by a cobalamin-dependent radical S -adenosylmethionine enzyme in cystobactamids biosynthesis.
Authors: Cui, J. / Wang, B. / Maurya, R.K. / Booker, S.J.
History
DepositionJan 25, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Radical SAM enzyme CysS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7177
Polymers73,1861
Non-polymers2,5316
Water7,350408
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-46 kcal/mol
Surface area23970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.450, 75.985, 77.045
Angle α, β, γ (deg.)90.00, 101.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Radical SAM enzyme CysS


Mass: 73186.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corallococcus sp. CA054B (bacteria) / Gene: D7V80_23740 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A3A8HCN5

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Non-polymers , 7 types, 414 molecules

#2: Chemical ChemComp-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C62H89CoN13O14P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Fe4S4
#4: Chemical ChemComp-5AD / 5'-DEOXYADENOSINE


Mass: 251.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S
#6: Chemical ChemComp-A1BUP / 2-({N-[(2R)-2,4-dihydroxy-3,3-dimethylbutanoyl]-beta-alanyl}amino)ethyl 4-amino-3-ethoxybenzoate


Mass: 425.476 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H31N3O7 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 408 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.22 Å3/Da / Density % sol: 44.56 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 100 mM MES pH 6.0, 25% w/v PEG6000, 200 mM lithium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03317 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 42639 / % possible obs: 98.9 % / Redundancy: 5.2 % / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.024 / Rrim(I) all: 0.055 / Χ2: 0.861 / Net I/σ(I): 10 / Num. measured all: 219601
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2-2.035.30.55321080.8290.9520.2570.6110.93799.2
2.03-2.075.30.47821230.8720.9650.2210.5280.95799.2
2.07-2.115.30.42321320.8910.9710.1970.4680.95899.3
2.11-2.155.20.35721420.9070.9750.1680.3960.94599.6
2.15-2.25.20.30521410.9310.9820.1430.3380.93799.8
2.2-2.255.10.25121630.9490.9870.1180.2790.99899.6
2.25-2.315.10.21620950.9630.9910.1030.240.98699.3
2.31-2.375.10.17921250.9760.9940.0850.1990.9799.3
2.37-2.4450.15421360.9810.9950.0740.1720.95198.8
2.44-2.524.90.13120990.9830.9960.0630.1460.9798.2
2.52-2.614.60.10620970.9860.9960.0540.1190.94496.5
2.61-2.714.60.08420730.9910.9980.0420.0950.92896.7
2.71-2.845.40.07121510.9950.9990.0330.0780.87699.2
2.84-2.995.40.05621230.9960.9990.0250.0610.82499.5
2.99-3.175.40.04521660.9970.9990.0210.050.76299.3
3.17-3.425.40.03421130.99810.0160.0380.71999.2
3.42-3.765.30.02621820.99810.0120.0290.67599.8
3.76-4.315.10.02221610.99810.0110.0250.6399.7
4.31-5.434.70.0220870.99910.010.0220.6295.7
5.43-505.40.02122220.99910.010.0240.67799.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→33.94 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1982 2000 4.72 %
Rwork0.1653 --
obs0.1669 42349 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→33.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5153 0 1 411 5565
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045357
X-RAY DIFFRACTIONf_angle_d0.6837305
X-RAY DIFFRACTIONf_dihedral_angle_d14.8242044
X-RAY DIFFRACTIONf_chiral_restr0.05785
X-RAY DIFFRACTIONf_plane_restr0.005974
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.2571300.22242628X-RAY DIFFRACTION90
2.05-2.110.26931420.21342847X-RAY DIFFRACTION97
2.11-2.170.27351450.21142920X-RAY DIFFRACTION99
2.17-2.240.2351420.19752877X-RAY DIFFRACTION99
2.24-2.320.21741440.18792913X-RAY DIFFRACTION99
2.32-2.410.20681440.18062903X-RAY DIFFRACTION99
2.41-2.520.21421420.17732869X-RAY DIFFRACTION98
2.52-2.650.23281390.17952804X-RAY DIFFRACTION96
2.65-2.820.21171440.17672916X-RAY DIFFRACTION99
2.82-3.040.21081450.17422920X-RAY DIFFRACTION99
3.04-3.340.22461460.17532928X-RAY DIFFRACTION99
3.34-3.820.19161450.14772938X-RAY DIFFRACTION100
3.83-4.820.15151460.12962931X-RAY DIFFRACTION99
4.82-33.940.14411460.13872955X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / 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)
11.5077-0.5771-0.2921.7612-0.39011.3774-0.2741.10040.0707-0.96280.47381.34620.4939-0.2782-0.40090.5098-0.1619-0.43620.69130.28830.53264.35996.0082-14.1466
22.31361.3193-1.09660.9252-1.44814.4046-0.04130.17310.51090.5507-0.17772.29921.7523-1.83820.13780.6767-0.2067-0.05780.48290.01441.3733-3.6309-6.50461.244
32.22820.20490.37042.5249-0.71011.83180.0540.00730.29510.1109-0.01070.53050.0339-0.00760.00790.13550.00510.0630.12020.01210.261816.468710.88110.8083
42.94730.4630.74593.13340.48522.80850.150.1904-0.14030.1601-0.1925-0.2082-0.04290.08810.06020.15020.00760.00210.14170.020.124532.2574-6.289217.333
51.1818-0.04550.13822.117-1.11651.09880.0446-0.1577-0.07890.4932-0.06150.1211-0.1388-0.0220.02240.2497-0.02260.05020.1648-0.01470.141619.8728-8.327924.9756
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 5:181)
2X-RAY DIFFRACTION2(chain A and resid 182:186)
3X-RAY DIFFRACTION3(chain A and resid 187:421)
4X-RAY DIFFRACTION4(chain A and resid 422:515)
5X-RAY DIFFRACTION5(chain A and resid 516:704)

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