PDB-8ubs: Crystal structure of NrdJ-1 split intein fusion

ID or keywords:

Entry

Database: PDB / ID: 8ubs

Title

Crystal structure of NrdJ-1 split intein fusion

Components

NrdJ-1

Keywords

SPLICING / Fusion of the split intein NrdJ-1.

Function / homology

FORMIC ACID

Function and homology information

Biological species

marine metagenome (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Kofoed, C. / Ye, X. / Jeffrey, P.D. / Muir, T.W.

Funding support

United States, European Union, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	2R01GM086868-25	United States
European Molecular Biology Organization (EMBO)	EMBO ALTF 1189-2020	European Union

Citation

Journal: To Be Published
Title: Cell surface sculpting using logic-gated protein actuators
Authors: Muir, T.W. / Kofoed, C. / Ye, X. / Jeffrey, P.

History

Deposition	Sep 24, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 9, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8ubs.cif.gz	314.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8ubs.ent.gz	213.1 KB	Display	PDB format
PDBx/mmJSON format	8ubs.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8ubs_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	8ubs_full_validation.pdf.gz	1.4 MB	Display
Data in XML	8ubs_validation.xml.gz	31.8 KB	Display
Data in CIF	8ubs_validation.cif.gz	42.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ub/8ubs ftp://data.pdbj.org/pub/pdb/validation_reports/ub/8ubs	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

Deposited unit

A: NrdJ-1

B: NrdJ-1

C: NrdJ-1

D: NrdJ-1

hetero molecules

68.2 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: NrdJ-1

hetero molecules

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

2

B: NrdJ-1

hetero molecules

defined by author
Evidence: gel filtration, mass spectrometry
17.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: NrdJ-1

hetero molecules

defined by author
Evidence: gel filtration, mass spectrometry
17 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: NrdJ-1

hetero molecules

defined by author
Evidence: gel filtration, mass spectrometry
17 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	48.793, 84.383, 174.709
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

#1: Protein	NrdJ-1 Mass: 16938.961 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Catalytically inactive fusion of split intein NrdJ-1 N and C fragments carrying C1A and N145A mutations. Source: (gene. exp.) marine metagenome (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH₂O₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Na
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 398 / Source method: isolated from a natural source / Formula: H₂O
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: 2.65 Å³/Da / Density % sol: 53.66 %
Crystal grow	Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 4.5 M sodium formate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.97242 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 5, 2022
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97242 Å / Relative weight: 1
Reflection	Resolution: 1.95→29.12 Å / Num. obs: 53184 / % possible obs: 99.8 % / Redundancy: 6.8 % / B_iso Wilson estimate: 26.5 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.128 / R_pim(I) all: 0.053 / R_rim(I) all: 0.139 / Net I/σ(I): 10.3
Reflection shell	Resolution: 1.95→2 Å / Redundancy: 6.6 % / R_merge(I) obs: 0.844 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3754 / CC_1/2: 0.808 / R_pim(I) all: 0.352 / R_rim(I) all: 0.916 / % possible all: 98.1

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Processing

Software

Name	Version	Classification
PHENIX	1.17_3644	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.95→29.12 Å / SU ML: 0.2097 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.3388
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.221	2665	5.02 %
R_work	0.1801	50434	-
obs	0.1822	53099	99.82 %

Solvent computation

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

Displacement parameters

B_iso mean: 36.26 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→29.12 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4724	0	25	398	5147

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0064	4889
X-RAY DIFFRACTION	f_angle_d	0.8015	6656
X-RAY DIFFRACTION	f_chiral_restr	0.0608	797
X-RAY DIFFRACTION	f_plane_restr	0.0043	858
X-RAY DIFFRACTION	f_dihedral_angle_d	21.4251	1812

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 (%)
1.95-1.99	0.2731	136	0.2279	2502	X-RAY DIFFRACTION	97.24
1.99-2.03	0.2686	118	0.2172	2649	X-RAY DIFFRACTION	100
2.03-2.07	0.2307	148	0.2069	2608	X-RAY DIFFRACTION	100
2.07-2.11	0.2468	128	0.1919	2664	X-RAY DIFFRACTION	100
2.11-2.16	0.2884	143	0.1831	2587	X-RAY DIFFRACTION	99.96
2.16-2.22	0.2254	130	0.177	2659	X-RAY DIFFRACTION	100
2.22-2.28	0.1965	142	0.1741	2592	X-RAY DIFFRACTION	100
2.28-2.34	0.2009	148	0.1703	2639	X-RAY DIFFRACTION	99.96
2.34-2.42	0.2611	133	0.1837	2631	X-RAY DIFFRACTION	99.96
2.42-2.51	0.2581	140	0.1902	2635	X-RAY DIFFRACTION	99.96
2.51-2.61	0.2486	124	0.2089	2656	X-RAY DIFFRACTION	100
2.61-2.73	0.2195	132	0.2005	2693	X-RAY DIFFRACTION	100
2.73-2.87	0.2822	142	0.2144	2656	X-RAY DIFFRACTION	99.96
2.87-3.05	0.2514	132	0.2016	2659	X-RAY DIFFRACTION	100
3.05-3.28	0.2338	151	0.1838	2650	X-RAY DIFFRACTION	100
3.28-3.61	0.1941	150	0.1566	2669	X-RAY DIFFRACTION	100
3.61-4.13	0.1611	155	0.1433	2701	X-RAY DIFFRACTION	100
4.14-5.2	0.1764	143	0.1314	2733	X-RAY DIFFRACTION	100
5.2-29.12	0.2471	170	0.2221	2851	X-RAY DIFFRACTION	99.44

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	7.1352330604	-3.2416107617	5.49503129488	6.6846754025	-2.75173918535	8.08646260403	0.226343832462	-0.0788781213424	-0.235122953283	-0.069895754753	-0.0437684250346	0.0805504313563	0.552295018733	-0.00778787001033	-0.0985776471723	0.179693483618	0.0146578405497	-0.00254462498455	0.127611514045	-0.0204029642348	0.201846343853	3.41445159586	-7.67589891672	3.19972062806
2	4.67498489934	-1.06668216918	1.53959934429	5.56019664102	1.63544924152	5.46432139634	-0.168895668768	-0.0113267947035	0.165517660007	0.306291859358	0.208842302828	-0.272456439044	-0.0197356035631	0.325273180025	-0.126615350223	0.162343494366	-0.0073066829994	-0.0648989028649	0.127860764805	0.0125403395184	0.190346545016	10.0961674593	-6.18514150788	3.40190491986
3	3.74663401723	-1.38195474775	0.383441092465	5.18472211417	1.73907786847	2.68702117012	-0.0905937892726	0.114299928626	-0.0218685963332	0.0284416127341	0.0161445708794	0.452878016796	0.0148809521631	-0.189422120644	0.0727249076156	0.147077348213	-0.0122861998366	0.0122784322057	0.196274728526	0.0276867951428	0.203246352533	-3.9880333258	-5.853260885	-8.30084810902
4	7.71567645502	-4.65751388039	-2.4876682646	7.92264167932	4.18285352621	8.47067112054	0.133935627265	0.463543168679	-0.0106401669502	-0.325669075583	0.0111425717619	-0.0607328602944	0.23498235645	-0.171075440973	-0.15977639458	0.151070076744	-0.0652067213048	-0.0132035688532	0.190534817918	0.036614218853	0.16300663335	4.90534138534	-5.10072261547	-16.6694318259
5	4.72040077698	0.266235464903	0.812873835082	2.11178132306	3.34705093188	5.3370569799	0.29862818293	-0.264864896085	-0.633016540232	0.917501949154	-0.0173721762014	-0.11594994286	1.08525120825	0.0437162628345	-0.242038180315	0.412530846044	-0.0508385595753	-0.0615482884743	0.230845064945	0.0274884781657	0.230990073088	7.13572026512	-18.12933171	-4.97441582539
6	2.60045359381	-1.81400624227	0.305927791879	2.4367276271	0.324994213902	2.23903948338	-0.103860717649	0.0135737080405	0.0641591833436	0.144721022202	0.0792634270842	-0.0248964159854	-0.00352935840955	0.0488588873278	0.00787202132561	0.156039842496	-0.0531150362001	-0.0176089635927	0.141926910334	0.0359268659561	0.164307000122	3.32586140932	-5.46159420437	-6.88635369251
7	3.95064675145	-1.66770169792	1.07384434149	5.85217029583	0.664731619443	3.83866297141	-0.0429010026145	0.0149035434732	0.617267952055	-0.260283255524	-0.0114057444962	0.175342796162	-0.89342779178	-0.492121920021	0.0373225997768	0.456064922367	0.105614482002	-0.0227929092822	0.237850179524	0.0266065256152	0.337773136352	19.7976151227	23.7476604488	-15.9509446232
8	3.18478956923	0.0918701910843	0.555308214026	2.85214477301	0.533378264514	3.12016464279	-0.00841728730848	0.0420446677414	0.168865704986	-0.0114669478837	0.0402249841492	-0.0280015390695	-0.311426505044	-0.136964153347	-0.0317845161852	0.16694850638	0.0183490727659	-0.000379924891972	0.126582651861	0.0353273380078	0.163625267533	21.3087934105	9.55460713463	-16.6779197539
9	6.08099942349	1.85657504548	1.38934234513	6.23875504797	1.49419403681	8.98569087527	-0.487193870575	0.858017113645	-0.28757904741	-0.579563803664	0.0775091076122	-0.0452487724686	-0.0787103748161	0.734621667935	0.326931126795	0.263097555448	-0.0442413293375	0.0484289928222	0.42630635381	0.0241466637605	0.230396291969	31.5079818151	-8.32161818617	14.1230587921
10	3.70475908973	0.65634965774	0.57556083308	2.25345112566	-0.419998094211	3.53860695506	-0.373063642465	0.815823714025	0.243548826458	-0.418296779934	0.173987514572	-0.121163468865	-0.423337499376	0.549718453527	0.157975254614	0.316863885352	-0.104977370804	-0.0133396293954	0.394252717676	0.0342746737428	0.190585997527	25.6954412253	-5.80842215437	11.044717434
11	5.88107123839	2.2583574627	0.672806106459	4.67696159178	-1.23026129055	4.92632806519	-0.176484122753	0.211301425662	-0.300827300628	-0.193040933001	0.00205391605811	-0.394263526831	0.0827839589519	0.487404547564	0.0930001775465	0.154369932045	0.0299349271551	0.0210427434851	0.288785420754	0.0434594142402	0.193070151869	34.6599362733	-7.28439184991	27.5579476475
12	4.97215873737	0.77635517539	1.31355328371	2.57512952228	0.744035771161	4.28834067003	-0.157148141203	-0.127894557853	0.229759620431	0.04986394547	0.0048697165583	-0.0962458175346	-0.15446185373	0.128366220487	0.245031089276	0.153155913294	-0.0100494880226	-0.0153847282593	0.181271287813	0.00841744008072	0.155505116766	27.1640717062	-3.88076372543	29.3105307351
13	4.71425655037	1.34827240295	2.25787105359	4.29983616585	3.93212281681	7.53199724738	0.0559068350486	-0.199154147984	-0.378197938713	0.0964088881457	-0.257311526351	0.178393808825	0.631895450226	-0.331164748874	0.0654781801863	0.219121813658	-0.0128734147209	0.0218612742316	0.146886509003	0.0372363256712	0.222937546159	22.6264633638	-14.4541975899	27.224107477
14	5.0810544723	1.26197472538	1.85481517801	1.09030499135	0.954801811672	3.99346215407	-0.280616249439	0.364568932932	0.157654660793	-0.154300841925	0.0513819351898	-0.0811030879757	-0.197317944382	0.414128363111	0.184795597695	0.180586306523	-0.0103599646488	0.00469854861825	0.193666836287	0.0313948085471	0.177858998309	29.4788989885	-4.94627011703	23.1405589537
15	6.55700010064	2.55049444999	1.09604596941	7.80202753984	1.37805295339	7.65039157446	-0.3045860943	-0.371459799972	1.44986389385	0.336908163996	0.0622909904161	0.36829128274	-1.09547902897	0.149653872395	0.21105504316	0.431260201168	-0.0300207066006	-0.0761008679808	0.274630964142	-0.0550520132705	0.576954461911	10.786200819	15.5673457128	41.5138372942
16	5.73098445456	-1.00023914406	1.19086602475	3.5871532309	-5.84190961612	9.77354790844	0.123833399318	-0.351375962591	0.967916446944	-0.155729802491	-0.352419243212	-0.197941223535	-0.145723074834	0.877481950797	0.28151783336	0.370427184751	-0.122561530722	-0.0530415046736	0.501696419237	-0.174077276827	0.53781157978	20.9216276339	10.8526929426	43.6444183699
17	3.39498374953	0.355819659865	2.22988323825	3.67115104787	-1.33548106331	2.14148782504	-0.181691994272	-0.00489147702975	0.472029139334	-0.0231703729331	-0.0115758362604	0.109279773489	-0.309398319455	-0.373828712333	0.139480015838	0.184489130283	-0.00814843635799	-0.00930645460421	0.250117782157	-0.00577209950627	0.263590798019	3.40539218431	1.72597417369	41.434036914
18	2.61652650941	-2.46993574112	2.86809990045	9.36366882955	-3.87480460377	9.09428459728	-0.0400986980558	0.121663414896	-0.232498269748	0.149662295686	0.0383380823492	0.0226700529228	0.167792869627	0.352123169461	0.0623715374285	0.145850855384	-0.011012564446	0.0266464845157	0.257691260809	-0.00291302923034	0.153292055582	12.1371688589	-6.72663628978	40.5469930399
19	3.88576745994	0.134146232304	2.77869084753	1.95615317597	-1.9047486972	5.56179512768	-0.0242983566751	-0.77726896676	0.317213246019	0.388394257517	-0.0914367617332	-0.0845429623518	-0.585572561766	0.0434074068801	0.162883906792	0.251837872595	-0.0169337331317	0.0212061717599	0.442872304223	-0.0970482696936	0.18631512338	8.43080829761	-1.30368027041	49.6028250272
20	5.8887964722	-0.439413073118	4.13846258402	2.44393541004	-0.471574163349	4.85185904091	-0.220766948981	0.166074168471	0.857689956048	-0.13428021038	0.0465609513346	-0.129965421313	-0.297204953874	0.330953148226	0.176764101477	0.271522949878	-0.0472616119595	0.00772369959696	0.212177602888	-0.0158810140548	0.307920044017	13.2929190045	6.51190852179	38.1899075519

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 17 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 18 through 56 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 57 through 79 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 80 through 103 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 104 through 111 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 112 through 151 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 2 through 56 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 57 through 151 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 2 through 16 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 17 through 56 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 57 through 74 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 75 through 97 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 98 through 113 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 114 through 151 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 2 through 29 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 30 through 56 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 57 through 79 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 80 through 103 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 104 through 124 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 125 through 151 )

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About Yorodumi

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Yorodumi