PDB-9n1b: Crystal structure of CysS from Corallococcus sp. CA054B with 5'-d...

ID or keywords:

Entry

Database: PDB / ID: 9n1b

Title

Crystal structure of CysS from Corallococcus sp. CA054B with 5'-deoxyadenosine, methionine, and pantetheinylated 3-methoxyl-4-amino benzoic acid substrate bound

Components

Radical SAM protein

Keywords

OXIDOREDUCTASE/SUBSTRATE / cystobactamids / radical S-adenosylmethionine methylase / cobalamin / OXIDOREDUCTASE / OXIDOREDUCTASE-SUBSTRATE complex

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: 1.75 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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Download

PDBx/mmCIF format	9n1b.cif.gz	348.4 KB	Display	PDBx/mmCIF format
PDB format	pdb9n1b.ent.gz		Display	PDB format
PDBx/mmJSON format	9n1b.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/n1/9n1b ftp://data.pdbj.org/pub/pdb/validation_reports/n1/9n1b	HTTPS FTP

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Related structure data

Related structure data	9n1cC 9n1dC 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 protein

hetero molecules

75.7 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)	56.044, 75.287, 77.015
Angle α, β, γ (deg.)	90.000, 100.750, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb

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Protein , 1 types, 1 molecules A

#1: Protein	Radical SAM protein 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, 606 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 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical	ChemComp-A1BUN / 2-({N-[(2R)-2,4-dihydroxy-3,3-dimethylbutanoyl]-beta-alanyl}amino)ethyl 4-amino-3-methoxybenzoate Mass: 411.449 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₉H₂₉N₃O₇ / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 599 / 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: 2.2 Å³/Da / Density % sol: 44.08 %
Crystal grow	Temperature: 296 K / Method: vapor diffusion, hanging drop Details: 100 mM MES pH6.0, 20% w/v PEG6000, 200 mM magnesium chloride

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97872 Å

Detector

Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 19, 2022

Radiation

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

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 1.75→50 Å / Num. obs: 62870 / % possible obs: 99.1 % / Redundancy: 7.7 % / CC_1/2: 0.997 / CC star: 0.999 / R_merge(I) obs: 0.07 / R_pim(I) all: 0.027 / R_rim(I) all: 0.075 / Χ²: 0.853 / Net I/σ(I): 8.2 / Num. measured all: 482585

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
1.75-1.78	7.7	0.513	3061	0.89	0.97	0.197	0.55	0.705	98.3
1.78-1.81	7.6	0.45	3122	0.927	0.981	0.173	0.482	0.734	98.4
1.81-1.85	7.7	0.394	3096	0.935	0.983	0.151	0.422	0.758	98.2
1.85-1.89	7.7	0.336	3113	0.955	0.988	0.129	0.36	0.801	98.2
1.89-1.93	7.7	0.344	3137	0.951	0.987	0.133	0.368	1.053	98.5
1.93-1.97	7.7	0.261	3088	0.971	0.993	0.1	0.28	0.885	98.8
1.97-2.02	7.7	0.208	3109	0.979	0.995	0.08	0.223	0.868	98.9
2.02-2.07	7.7	0.198	3152	0.979	0.995	0.077	0.213	1.064	98.8
2.07-2.14	7.7	0.162	3111	0.986	0.997	0.062	0.173	0.914	98.8
2.14-2.2	7.7	0.133	3142	0.989	0.997	0.051	0.143	0.886	99
2.2-2.28	7.6	0.14	3138	0.987	0.997	0.055	0.15	1.209	98.9
2.28-2.38	7.7	0.095	3127	0.994	0.999	0.037	0.102	0.843	99.4
2.38-2.48	7.7	0.086	3165	0.994	0.999	0.033	0.092	0.866	99.5
2.48-2.61	7.7	0.077	3137	0.994	0.998	0.03	0.083	0.933	99.4
2.61-2.78	7.7	0.067	3196	0.995	0.999	0.026	0.071	1.007	99.7
2.78-2.99	7.7	0.052	3154	0.996	0.999	0.02	0.056	0.912	99.6
2.99-3.29	7.7	0.039	3179	0.998	0.999	0.015	0.042	0.777	99.8
3.29-3.77	7.7	0.029	3192	0.998	1	0.011	0.031	0.73	99.9
3.77-4.75	7.6	0.021	3197	0.999	1	0.008	0.023	0.573	99.7
4.75-50	7.5	0.021	3254	0.998	1	0.008	0.023	0.535	99.6

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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: 1.75→33.7 Å / SU ML: 0.1815 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.5873
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1842	3136	5 %
R_work	0.1527	59607	-
obs	0.1542	62743	98.37 %

Solvent computation

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

Displacement parameters

B_iso mean: 26 Å²

Refinement step

Cycle: LAST / Resolution: 1.75→33.7 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5014	0	157	599	5770

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0048	5404
X-RAY DIFFRACTION	f_angle_d	0.7755	7372
X-RAY DIFFRACTION	f_chiral_restr	0.0547	791
X-RAY DIFFRACTION	f_plane_restr	0.0058	982
X-RAY DIFFRACTION	f_dihedral_angle_d	15.0482	2054

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 (%)
1.75-1.77	0.2601	122	0.2218	2334	X-RAY DIFFRACTION	85.9
1.77-1.8	0.2446	143	0.2015	2708	X-RAY DIFFRACTION	97.47
1.8-1.83	0.2157	141	0.1917	2655	X-RAY DIFFRACTION	97.32
1.83-1.87	0.1891	141	0.1868	2689	X-RAY DIFFRACTION	98.37
1.87-1.9	0.2514	140	0.1952	2675	X-RAY DIFFRACTION	98.19
1.9-1.94	0.2455	142	0.2023	2689	X-RAY DIFFRACTION	97.99
1.94-1.98	0.185	141	0.178	2695	X-RAY DIFFRACTION	98.17
1.98-2.03	0.2313	144	0.1703	2726	X-RAY DIFFRACTION	98.59
2.03-2.08	0.2156	143	0.1739	2711	X-RAY DIFFRACTION	98.89
2.08-2.14	0.1991	143	0.1639	2709	X-RAY DIFFRACTION	98.96
2.14-2.2	0.2057	143	0.164	2739	X-RAY DIFFRACTION	99.04
2.2-2.27	0.2263	143	0.168	2686	X-RAY DIFFRACTION	98.85
2.27-2.35	0.1762	142	0.1582	2733	X-RAY DIFFRACTION	98.93
2.35-2.45	0.185	146	0.1484	2745	X-RAY DIFFRACTION	99.42
2.45-2.56	0.1887	144	0.1481	2742	X-RAY DIFFRACTION	99.62
2.56-2.69	0.1684	143	0.1507	2719	X-RAY DIFFRACTION	99.41
2.69-2.86	0.1637	145	0.1526	2760	X-RAY DIFFRACTION	99.76
2.86-3.08	0.1881	145	0.1487	2752	X-RAY DIFFRACTION	99.76
3.08-3.39	0.1979	144	0.1532	2743	X-RAY DIFFRACTION	99.9
3.39-3.88	0.1568	147	0.128	2783	X-RAY DIFFRACTION	99.9
3.88-4.89	0.1531	146	0.1192	2779	X-RAY DIFFRACTION	99.69
4.89-33.7	0.1509	148	0.1406	2835	X-RAY DIFFRACTION	99.73

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	1.34580627775	0.322747691712	-0.71732188814	1.34275991505	-0.238511385955	1.19198089793	-0.216517319627	0.60219406083	0.0745415073201	-0.426404542002	0.38981917291	0.478349164148	0.182787257806	-0.386432340661	-0.071020866848	0.20803175757	-0.122226358617	-0.111302261316	0.382943653836	0.116587293183	0.248777698603	3.89846688686	8.0565301886	-14.0636218389
2	5.82679268173	3.18745179306	-1.37594277473	3.39031433597	-1.26542044556	0.484475242244	-0.444539138364	0.734121203066	-1.26227645104	-0.987002746768	0.287437355818	-0.0294279972024	1.38151461447	-1.42230014669	0.153029888799	0.513448947366	-0.156675790699	0.0347679842586	0.395424893714	-0.0844898561919	0.435940475012	-3.8001163231	-4.6400127398	1.37388699569
3	1.16380990241	0.293327397293	-0.10124819702	1.00305470731	0.0872615356003	0.695701862914	0.00329524674356	-0.0316968736524	0.138423137068	0.143359022104	-0.0217958095169	0.146729519196	0.0436077374229	-0.0468363230369	0.00820567239609	0.119204011877	0.000123629319934	0.0255067232553	0.0937303024927	0.00240373211285	0.12056295906	16.0871042591	12.8464560345	10.863525504
4	1.80915875707	0.286735247226	0.716240150025	1.61638464759	0.309772876773	2.97495738392	0.0381907996585	0.00582749482342	-0.0582180528426	0.135580251041	-0.0698401782638	-0.120642804118	-0.0552611478602	0.0580483609646	0.0101971686259	0.103365948381	0.00640057488575	-0.01427916294	0.081637656606	0.0030415328982	0.102594054416	32.1903240924	-4.23344406079	17.323708533
5	0.724089606177	-0.0793142229366	0.2421118419	1.37972564568	-0.968818239316	0.792753310223	0.0338398145288	-0.14391820302	-0.134802814642	0.323914156952	0.0180597829375	0.0586906551904	-0.0848194626596	-0.031936909549	-0.02786123483	0.174563540287	0.00333977520927	0.0115551408011	0.136705700715	-0.00171074903715	0.10080636507	20.0109765671	-6.20579289509	25.215385847

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A

ID	Refine TLS-ID	Selection details	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	(chain A and resid 6:181)	A	6 - 181	1 - 176
2	2	(chain A and resid 182:186)	A	182 - 186	177 - 181
3	3	(chain A and resid 187:421)	A	187 - 421	182 - 416
4	4	(chain A and resid 422:515)	A	422 - 515	417 - 510
5	5	(chain A and resid 516:704)	A - E	516 - 704	511 - 630

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