PDB-9cg1: DUF512 protein from Clostridium sporogenes

ID or keywords:

Entry

Database: PDB / ID: 9cg1

Title

DUF512 protein from Clostridium sporogenes

Components

Radical SAM protein

Keywords

OXIDOREDUCTASE / radical S-adenosylmethionine enzyme / DUF512 / PDZ domain

Function / homology

Function and homology information

Domain of unknown function DUF512 / Protein of unknown function (DUF512) / Putative radical SAM, N-terminal / Radical SAM-like domain / PDZ domain 6 / PDZ domain / PDZ superfamily / Aldolase-type TIM barrel
Similarity search - Domain/homology

Biological species

Clostridium sporogenes (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.68 Å

Authors

Wang, B. / Radle, M.I. / Peduzzi, O. / Solinski, A. / Knox, H.L. / Cui, J. / Maurya, R. / Yennawar, N. / Booker, S.J.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: DUF512 protein from Clostridium sporogenes
Authors: Wang, B. / Radle, M.I. / Peduzzi, O. / Solinski, A. / Knox, H.L. / Cui, J. / Maurya, R. / Yennawar, N. / Booker, S.J.

History

Deposition	Jun 28, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 5, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9cg1.cif.gz	215.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9cg1.ent.gz	169.3 KB	Display	PDB format
PDBx/mmJSON format	9cg1.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/cg/9cg1 ftp://data.pdbj.org/pub/pdb/validation_reports/cg/9cg1	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#134 - Feb 2011 Integrin similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #194 - Feb 2016 Designer Insulins similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1) #259 - Jul 2021 Designed Proteins and Citizen Science similarity (1)

Deposited unit

A: Radical SAM protein

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	56.670, 59.302, 81.059
Angle α, β, γ (deg.)	90.00, 109.82, 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 protein / DUF512 protein Mass: 51437.719 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium sporogenes (bacteria) / Gene: CGS26_13040, FDB81_14220 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0AAE4Z2Q4

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Non-polymers , 7 types, 503 molecules

#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-BO3 / BORIC ACID Mass: 61.833 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BH₃O₃
#4: Chemical	ChemComp-B12 / COBALAMIN Mass: 1330.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆₂H₈₉CoN₁₃O₁₄P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-SF4 / IRON/SULFUR CLUSTER Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe₄S₄ / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical	ChemComp-IMD / IMIDAZOLE Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₅N₂
#7: Chemical	ChemComp-SA8 / S-5'-AZAMETHIONINE-5'-DEOXYADENOSINE / 5'-[N-[(3S)-3-AMINO-3-CARBOXYPROPYL]-N-METHYLAMINO]-5'-DEOXYADENOSINE Mass: 381.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₅H₂₃N₇O₅ / Feature type: SUBJECT OF INVESTIGATION
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 495 / 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: 2.39 Å³/Da / Density % sol: 48.6 %
Crystal grow	Temperature: 296 K / Method: vapor diffusion, hanging drop Details: 100 mM sodium malonate, imidazole, and boric acid buffer (in the molar ratios 2:3:3), pH 5.0, 25% (w/v) PEG1500

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 23-ID-B / Wavelength: 1.03317 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 22, 2021

Radiation

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

Radiation wavelength

Wavelength: 1.03317 Å / Relative weight: 1

Reflection

Resolution: 1.68→50 Å / Num. obs: 85548 / % possible obs: 99.9 % / Redundancy: 6.4 % / CC_1/2: 0.994 / CC star: 0.999 / R_merge(I) obs: 0.058 / R_pim(I) all: 0.025 / R_rim(I) all: 0.063 / Χ²: 0.833 / Net I/σ(I): 11

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
1.68-1.71	6.2	0.524	2844	0.905	0.975	0.226	0.572	0.79	99.2
1.71-1.74	6.4	0.451	2881	0.929	0.981	0.191	0.491	0.837	99.9
1.74-1.77	6.6	0.385	2858	0.95	0.987	0.161	0.418	0.84	99.9
1.77-1.81	6.6	0.332	2817	0.959	0.989	0.139	0.361	0.853	100
1.81-1.85	6.6	0.277	2880	0.967	0.992	0.116	0.301	0.878	100
1.85-1.89	6.4	0.23	2877	0.976	0.994	0.098	0.251	0.915	99.9
1.89-1.94	5.9	0.208	2863	0.972	0.993	0.093	0.228	1.071	99.8
1.94-1.99	6.3	0.157	2862	0.986	0.996	0.067	0.171	0.937	99.9
1.99-2.05	6	0.128	2889	0.988	0.997	0.057	0.14	0.903	100
2.05-2.12	5.8	0.114	2843	0.99	0.997	0.051	0.125	1.034	99.8
2.12-2.19	6.9	0.093	2881	0.994	0.999	0.038	0.101	0.874	100
2.19-2.28	6.4	0.086	2870	0.994	0.998	0.037	0.094	1.043	99.8
2.28-2.38	6.9	0.067	2871	0.996	0.999	0.027	0.072	0.794	100
2.38-2.51	6.8	0.058	2856	0.997	0.999	0.024	0.063	0.761	100
2.51-2.67	6.5	0.049	2898	0.997	0.999	0.021	0.054	0.739	100
2.67-2.87	6.2	0.041	2886	0.998	0.999	0.018	0.045	0.655	99.9
2.87-3.16	6.4	0.035	2899	0.998	0.999	0.015	0.038	0.581	100
3.16-3.62	7	0.031	2865	0.997	0.999	0.013	0.033	0.577	99.9
3.62-4.56	6.7	0.031	2954	0.997	0.999	0.013	0.034	0.65	99.9
4.56-50	6.3	0.042	2972	0.993	0.998	0.018	0.046	1.02	99.9

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Processing

Software

Name	Version	Classification
PHENIX	(1.19.2_4158: ???)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.68→46.81 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.9 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.198	2986	3.49 %
R_work	0.158	-	-
obs	0.16	85548	75.6 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.68→46.81 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3614	0	150	495	4259

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	3943
X-RAY DIFFRACTION	f_angle_d	1.073	5348
X-RAY DIFFRACTION	f_dihedral_angle_d	15.671	1592
X-RAY DIFFRACTION	f_chiral_restr	0.07	595
X-RAY DIFFRACTION	f_plane_restr	0.009	731

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 (%)
1.68-1.71	0.3571	89	0.2867	2404	X-RAY DIFFRACTION	46
1.71-1.74	0.2561	92	0.2541	2571	X-RAY DIFFRACTION	50
1.74-1.77	0.2577	97	0.2268	2611	X-RAY DIFFRACTION	50
1.77-1.8	0.2264	91	0.1995	2684	X-RAY DIFFRACTION	51
1.8-1.84	0.1837	97	0.1896	2690	X-RAY DIFFRACTION	52
1.84-1.88	0.2287	97	0.1705	2803	X-RAY DIFFRACTION	54
1.88-1.92	0.2135	95	0.1824	2869	X-RAY DIFFRACTION	55
1.92-1.97	0.1816	112	0.1761	3097	X-RAY DIFFRACTION	59
1.97-2.02	0.2263	122	0.1771	3296	X-RAY DIFFRACTION	64
2.02-2.08	0.2087	115	0.1623	3419	X-RAY DIFFRACTION	66
2.08-2.15	0.1934	152	0.149	3964	X-RAY DIFFRACTION	76
2.15-2.23	0.1807	167	0.1471	4393	X-RAY DIFFRACTION	85
2.23-2.32	0.1885	165	0.1515	4589	X-RAY DIFFRACTION	89
2.32-2.42	0.2308	182	0.1507	5004	X-RAY DIFFRACTION	96
2.42-2.55	0.2197	180	0.1509	5174	X-RAY DIFFRACTION	99
2.55-2.71	0.2238	193	0.1606	5186	X-RAY DIFFRACTION	99
2.71-2.92	0.1818	192	0.1598	5126	X-RAY DIFFRACTION	99
2.92-3.21	0.2059	178	0.1626	5181	X-RAY DIFFRACTION	100
3.21-3.68	0.1974	199	0.1515	5159	X-RAY DIFFRACTION	99
3.68-4.63	0.1557	180	0.13	5162	X-RAY DIFFRACTION	99
4.64-46.81	0.1845	191	0.1584	5180	X-RAY DIFFRACTION	100

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	2.4491	0.0123	0.4958	2.5806	0.0541	2.8033	0.0495	-0.1814	0.3681	0.0859	-0.1761	0.2494	-0.316	-0.0771	0.1254	0.1569	-0.0152	0.0377	0.1622	-0.0281	0.1913	-19.5484	47.0651	44.044
2	2.5357	0.6293	0.5754	1.8768	-0.302	1.7285	0.0862	-0.3259	0.0023	0.3542	-0.1118	0.2315	0.0736	-0.1024	0.0391	0.1948	-0.0466	0.0431	0.1433	-0.0142	0.1403	-12.3424	44.77	48.2961
3	3.5103	-1.5691	-0.026	3.729	0.4673	2.3355	0.0484	-0.4176	0.3301	0.2922	0.0846	0.1887	-0.002	0.0409	-0.0886	0.1721	-0.0608	0.0385	0.1786	-0.0408	0.2231	-18.4865	39.5491	46.7495
4	0.7266	0.2303	-0.0543	0.962	0.2086	1.3795	0.0463	-0.0005	0.0682	0.0997	-0.0588	0.1869	-0.0801	-0.2619	0.0093	0.0948	0.0053	-0.0007	0.1111	-0.0018	0.176	-7.1139	57.114	30.3257
5	2.0459	0.0564	-0.6562	1.3233	-0.5381	3.3589	0.0025	-0.1682	0.1474	0.0996	-0.0311	0.0174	-0.0215	-0.0278	0.0239	0.0853	-0.0057	-0.0154	0.0588	-0.0148	0.1015	5.6356	52.3274	37.8216
6	1.8679	-0.1811	0.0406	3.2973	-0.5932	1.5365	-0.1324	-0.1922	0.5341	0.1447	-0.0283	-0.1348	-0.2774	0.226	0.1282	0.1298	0.0131	-0.0477	0.121	-0.058	0.2109	11.3112	56.9488	36.2486
7	1.9495	-0.6763	0.7433	1.3692	0.311	2.7506	-0.0896	0.0661	0.1201	0.05	0.027	-0.1956	0.0709	0.1984	0.0283	0.0568	0.0024	0.0016	0.0659	0.0151	0.0986	14.4616	47.3058	27.9462
8	1.8418	-0.7063	0.4984	2.099	0.8867	1.4682	0.006	0.4161	0.9835	-0.6494	-0.1563	-0.4088	-0.4635	0.1532	0.1292	0.206	0.0386	0.0069	0.1582	0.1045	0.2203	4.421	60.4696	12.0035
9	1.6783	-0.9845	1.6243	2.8157	-1.7225	4.809	-0.0044	0.5887	0.3428	-0.0187	-0.2151	-0.8906	-0.1056	0.6142	0.1201	0.0757	0.0238	0.1126	0.2261	0.0804	0.0756	18.8114	44.7292	13.7384
10	3.4966	-1.4092	1.2896	2.877	-0.9173	2.8905	-0.0656	0.0407	0.0364	0.0245	0.0222	-0.1763	0.1152	0.1512	0.0191	0.0694	0.011	0.0219	0.0815	0.0099	0.056	16.5697	37.4465	23.5716
11	3.4193	0.2347	-0.1714	2.9729	-0.979	3.2381	0.0129	0.0326	-0.2725	0.0402	-0.1137	-0.157	0.2472	-0.0549	0.096	0.1265	0.0149	-0.0198	0.1012	-0.003	0.0769	7.4088	35.7414	17.8257
12	3.1936	2.8733	1.532	2.5482	1.8184	0.9947	0.3178	0.1613	-0.83	0.2894	0.0002	-0.7677	0.7825	-0.217	-0.2221	0.3225	-0.0479	-0.0606	0.1764	-0.0292	0.1384	-2.8087	25.4348	12.9637
13	1.3458	0.4686	0.3421	2.8307	1.4219	1.5442	-0.0694	0.2923	-0.0902	-0.3156	-0.0077	0.0325	0.1005	-0.046	0.077	0.165	-0.015	0.0073	0.233	-0.0135	0.0694	-7.5274	34.4534	3.4551
14	2.9245	0.1085	-0.2984	2.52	0.1474	1.025	-0.022	0.2514	0.0622	-0.1857	-0.0398	0.2526	-0.0177	-0.3634	0.0754	0.0814	0.0005	-0.0233	0.2035	-0.0254	0.108	-15.8072	44.1181	11.0467
15	1.2379	-0.1697	-0.5751	2.0139	0.6415	1.4283	-0.0562	0.0412	-0.0373	0.1233	-0.1379	0.3611	0.2849	-0.4673	0.144	0.1348	-0.0729	0.0197	0.2718	-0.0544	0.1335	-16.9177	35.2438	11.1249
16	3.7779	-0.0215	1.4195	4.7237	1.9398	6.5973	0.2756	0.3201	-0.6787	-0.4621	-0.0805	0.1828	0.9718	-0.5205	0.0235	0.3908	-0.3052	0.1757	0.486	-0.1317	0.1897	-20.6528	22.3409	6.8832

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 1:32)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 33:55)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 56:71)
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 72:119)
5	X-RAY DIFFRACTION	5	(CHAIN A AND RESID 120:158)
6	X-RAY DIFFRACTION	6	(CHAIN A AND RESID 159:178)
7	X-RAY DIFFRACTION	7	(CHAIN A AND RESID 179:221)
8	X-RAY DIFFRACTION	8	(CHAIN A AND RESID 222:236)
9	X-RAY DIFFRACTION	9	(CHAIN A AND RESID 237:251)
10	X-RAY DIFFRACTION	10	(CHAIN A AND RESID 252:270)
11	X-RAY DIFFRACTION	11	(CHAIN A AND RESID 271:295)
12	X-RAY DIFFRACTION	12	(CHAIN A AND RESID 296:313)
13	X-RAY DIFFRACTION	13	(CHAIN A AND RESID 314:360)
14	X-RAY DIFFRACTION	14	(CHAIN A AND RESID 361:411)
15	X-RAY DIFFRACTION	15	(CHAIN A AND RESID 412:438)
16	X-RAY DIFFRACTION	16	(CHAIN A AND RESID 439:443)

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