PDB-9n1d: Crystal structure of CysS from Corallococcus sp. CA054B with 5'-d...

ID or keywords:

Entry

Database: PDB / ID: 9n1d

Title

Crystal structure of CysS from Corallococcus sp. CA054B with 5'-deoxyadenosine and methionine bound

Components

Radical SAM enzyme CysS

Keywords

OXIDOREDUCTASE / Cystobactamids / radical S-adenosylmethionine methylase / cobalamin

Function / homology

5'-DEOXYADENOSINE / COBALAMIN / METHIONINE / IRON/SULFUR CLUSTER / :

Function and homology information

Biological species

Corallococcus sp. CA054B (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.94 Å

Authors

Wang, B. / Cui, J. / Booker, S.J.

Funding support

United States, 1items

Citation

Journal: 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

Deposition	Jan 25, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 28, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9n1d.cif.gz	289.4 KB	Display	PDBx/mmCIF format
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PDBx/mmJSON format	9n1d.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/n1/9n1d ftp://data.pdbj.org/pub/pdb/validation_reports/n1/9n1d	HTTPS FTP

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Related structure data

Related structure data	9n1bC 9n1cC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Radical SAM enzyme CysS

hetero molecules

75.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	59.283, 77.816, 77.039
Angle α, β, γ (deg.)	90.00, 110.89, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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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 , 6 types, 548 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 / Feature type: SUBJECT OF INVESTIGATION
#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-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 543 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.27 Å³/Da / Density % sol: 45.76 %
Crystal grow	Temperature: 296 K / Method: vapor diffusion, hanging drop Details: 100 mM MES pH6.0, 15% w/v PEG6000, 200 mM sodium chloride

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 8.2.2 / Wavelength: 1.0358 Å

Detector

Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 20, 2022

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.0358 Å / Relative weight: 1

Reflection

Resolution: 1.94→50 Å / Num. obs: 68013 / % possible obs: 99.9 % / Redundancy: 3.4 % / CC_1/2: 0.978 / CC star: 0.994 / R_merge(I) obs: 0.071 / R_pim(I) all: 0.045 / R_rim(I) all: 0.084 / Χ²: 0.756 / Net I/σ(I): 9.9

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.95-1.98	3	0.522	2408	0.753	0.927	0.36	0.637	0.709	99.9
1.98-2.02	3.1	0.305	2378	0.857	0.961	0.205	0.369	0.646	99.9
2.02-2.06	3.4	0.267	2417	0.893	0.971	0.17	0.317	0.687	100
2.06-2.1	3.5	0.226	2372	0.923	0.98	0.141	0.267	0.691	100
2.1-2.15	3.5	0.207	2410	0.934	0.983	0.13	0.245	0.689	100
2.15-2.2	3.5	0.188	2422	0.945	0.986	0.118	0.223	0.702	100
2.2-2.25	3.4	0.292	2356	0.844	0.957	0.184	0.346	1.742	100
2.25-2.31	3.4	0.242	2401	0.88	0.968	0.153	0.287	1.795	99.9
2.31-2.38	3.4	0.115	2419	0.967	0.992	0.073	0.136	0.684	99.7
2.38-2.46	3.3	0.097	2404	0.973	0.993	0.063	0.115	0.654	99.9
2.46-2.54	3.1	0.082	2391	0.977	0.994	0.056	0.1	0.629	100
2.54-2.65	3.3	0.067	2415	0.985	0.996	0.043	0.08	0.588	100
2.65-2.77	3.6	0.061	2386	0.985	0.996	0.037	0.071	0.574	100
2.77-2.91	3.5	0.052	2424	0.989	0.997	0.032	0.061	0.572	100
2.91-3.1	3.5	0.046	2410	0.987	0.997	0.029	0.054	0.574	99.7
3.1-3.33	3.4	0.041	2412	0.986	0.997	0.026	0.049	0.574	99.9
3.33-3.67	3.1	0.04	2410	0.984	0.996	0.027	0.048	0.703	99.8
3.67-4.2	3.4	0.038	2425	0.989	0.997	0.024	0.045	0.681	99.9
4.2-5.29	3.5	0.036	2444	0.989	0.997	0.022	0.042	0.618	99.9
5.29-50	3.3	0.038	2487	0.989	0.997	0.025	0.046	0.586	99.9

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
HKL-2000		data scaling
HKL-2000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.94→37.85 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.5 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2043	2885	4.24 %
R_work	0.1595	-	-
obs	0.1614	68013	71.29 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.94→37.85 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5155	0	1	548	5704

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	5387
X-RAY DIFFRACTION	f_angle_d	0.799	7358
X-RAY DIFFRACTION	f_dihedral_angle_d	14.675	2063
X-RAY DIFFRACTION	f_chiral_restr	0.05	799
X-RAY DIFFRACTION	f_plane_restr	0.006	982

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.94-1.97	0.2763	78	0.2319	1731	X-RAY DIFFRACTION	40
1.97-2	0.2509	85	0.2048	2114	X-RAY DIFFRACTION	49
2-2.04	0.2324	105	0.1895	2153	X-RAY DIFFRACTION	50
2.04-2.08	0.2309	94	0.185	2200	X-RAY DIFFRACTION	50
2.08-2.12	0.2495	102	0.1891	2240	X-RAY DIFFRACTION	52
2.12-2.17	0.2401	92	0.1763	2319	X-RAY DIFFRACTION	53
2.17-2.22	0.233	103	0.203	2381	X-RAY DIFFRACTION	54
2.22-2.27	0.2593	109	0.2266	2433	X-RAY DIFFRACTION	56
2.27-2.34	0.2309	114	0.1796	2672	X-RAY DIFFRACTION	62
2.34-2.4	0.2674	128	0.1693	2974	X-RAY DIFFRACTION	68
2.41-2.48	0.2344	133	0.1649	3034	X-RAY DIFFRACTION	70
2.48-2.57	0.2189	137	0.1622	3283	X-RAY DIFFRACTION	75
2.57-2.67	0.2128	170	0.1602	3611	X-RAY DIFFRACTION	83
2.67-2.8	0.2201	164	0.1634	3796	X-RAY DIFFRACTION	88
2.8-2.94	0.2536	182	0.1621	3959	X-RAY DIFFRACTION	91
2.94-3.13	0.209	184	0.1643	4071	X-RAY DIFFRACTION	93
3.13-3.37	0.2186	174	0.1576	3961	X-RAY DIFFRACTION	92
3.37-3.71	0.1813	178	0.1539	3804	X-RAY DIFFRACTION	87
3.71-4.24	0.17	185	0.1378	4070	X-RAY DIFFRACTION	94
4.24-5.34	0.1564	182	0.1308	4138	X-RAY DIFFRACTION	96
5.35-37.85	0.171	186	0.1447	4184	X-RAY DIFFRACTION	96

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	2.429	-0.1517	0.0813	1.7287	-0.1927	2.1614	0.0466	0.3326	-0.1291	-0.3297	-0.0514	0.1258	0.3578	0.0762	0.0102	0.1984	0.0406	-0.0016	0.1343	-0.0203	0.1107	9.9152	5.4283	-19.4779
2	1.5801	-0.1964	1.1464	0.9218	-0.3852	1.9694	-0.0338	-0.1456	0.0463	0.0572	0.0581	0.0911	-0.1016	-0.2816	-0.028	0.0915	0.0397	0.053	0.094	0.0126	0.118	12.4577	10.991	7.8462
3	1.205	-0.0664	0.5952	1.554	-0.9019	0.7207	0.2814	0.1353	0.0836	0.1094	-0.1844	-0.0221	-0.007	0.1205	-0.0309	0.1076	0.0551	0.0355	0.073	-0.0033	0.1317	31.4037	1.5157	12.798
4	2.9384	0.2688	0.4936	2.5756	0.3348	2.7453	-0.0581	0.1772	-0.0435	-0.0414	0.0475	-0.188	-0.1254	0.1541	0.0121	0.0833	0.0042	0.0185	0.0641	0.0051	0.1041	31.3681	-9.2	15.1553
5	0.309	-0.0933	0.014	1.432	-1.1591	1.8891	0.0359	-0.0645	-0.0451	0.2003	-0.0054	0.0029	0.065	-0.0684	-0.0481	0.0926	-0.0103	0.0049	0.1103	0.0029	0.1305	17.2546	-8.9555	23.1604

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 5:163)
2	X-RAY DIFFRACTION	2	(chain A and resid 164:396)
3	X-RAY DIFFRACTION	3	(chain A and resid 397:446)
4	X-RAY DIFFRACTION	4	(chain A and resid 447:515)
5	X-RAY DIFFRACTION	5	(chain A and resid 516:704)

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