PDB-8t7j: Oxygen- and PLP-dependent Cap15 holoenzyme bound with phosphate anion

ID or keywords:

Entry

Database: PDB / ID: 8t7j

Title

Oxygen- and PLP-dependent Cap15 holoenzyme bound with phosphate anion

Components

Putative selenocysteine synthase

Keywords

BIOSYNTHETIC PROTEIN / pyridoxal 5'-phosphate / monooxygenase-decarboxylase / type I fold

Function / homology

L-seryl-tRNA selenium transferase-like / L-seryl-tRNA selenium transferase / catalytic activity / metabolic process / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / PHOSPHATE ION / Putative selenocysteine synthase

Function and homology information

Biological species

Streptomyces sp. SANK 62799 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Daniel-Ivad, P. / Ryan, K.S.

Funding support

1items

Citation

Journal: Biochemistry / Year: 2023
Title: Structure of the Oxygen, Pyridoxal Phosphate-Dependent Capuramycin Biosynthetic Protein Cap15.
Authors: Daniel-Ivad, P.G. / Van Lanen, S. / Ryan, K.S.

History

Deposition	Jun 20, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 23, 2023	Provider: repository / Type: Initial release
Revision 1.1	Sep 13, 2023	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Nov 15, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8t7j.cif.gz	616.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8t7j.ent.gz	421.8 KB	Display	PDB format
PDBx/mmJSON format	8t7j.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8t7j_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	8t7j_full_validation.pdf.gz	1.7 MB	Display
Data in XML	8t7j_validation.xml.gz	52.1 KB	Display
Data in CIF	8t7j_validation.cif.gz	70.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/t7/8t7j ftp://data.pdbj.org/pub/pdb/validation_reports/t7/8t7j	HTTPS FTP

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Related structure data

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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Putative selenocysteine synthase

B: Putative selenocysteine synthase

C: Putative selenocysteine synthase

D: Putative selenocysteine synthase

hetero molecules

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

1

A: Putative selenocysteine synthase

B: Putative selenocysteine synthase

C: Putative selenocysteine synthase

D: Putative selenocysteine synthase

hetero molecules

A: Putative selenocysteine synthase

B: Putative selenocysteine synthase

C: Putative selenocysteine synthase

D: Putative selenocysteine synthase

hetero molecules

defined by author
Evidence: gel filtration, predicted MW of 300 kDa, expected value 336 kDa, broad elution
339 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	142.590, 220.986, 96.735
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁
Space group name Hall	C2c2
Symmetry operation	#1: x,y,z #2: x,-y,-z #3: -x,y,-z+1/2 #4: -x,-y,z+1/2 #5: x+1/2,y+1/2,z #6: x+1/2,-y+1/2,-z #7: -x+1/2,y+1/2,-z+1/2 #8: -x+1/2,-y+1/2,z+1/2

#1: Protein	Putative selenocysteine synthase Mass: 42283.816 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. SANK 62799 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: E1CG36
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO₄ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.1 Å³/Da / Density % sol: 42 % / Description: parallelepiped, yellow
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.2 M sodium acetate, 17 % polyethylene glycol 3350, 10-15 mg/mL Cap15 Temp details: ambient variance

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97946 Å / Relative weight: 1
Reflection	Resolution: 2.4→38.9 Å / Num. obs: 60031 / % possible obs: 99.51 % / Redundancy: 13.5 % / B_iso Wilson estimate: 50.89 Å² / CC_1/2: 1 / R_merge(I) obs: 0.09 / R_pim(I) all: 0.025 / R_rim(I) all: 0.093 / Χ²: 1 / Net I/σ(I): 19.3
Reflection shell	Resolution: 2.4→2.46 Å / Redundancy: 13 % / R_merge(I) obs: 1.501 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4126 / CC_1/2: 0.881 / R_pim(I) all: 0.462 / R_rim(I) all: 1.562 / Χ²: 0.9 / % possible all: 99.38

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Processing

Software

Name	Version	Classification
PHENIX	1.19_4092	refinement
Blu-Ice		data collection
XDS		data reduction
Aimless		data scaling
PHASER		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.4→38.9 Å / SU ML: 0.358 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.0065
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2677	1991	3.33 %
R_work	0.2243	57772	-
obs	0.2257	59763	99.06 %

Solvent computation

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

Displacement parameters

B_iso mean: 72.5 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→38.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9762	0	28	223	10013

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	9948
X-RAY DIFFRACTION	f_angle_d	0.4819	13596
X-RAY DIFFRACTION	f_chiral_restr	0.0424	1596
X-RAY DIFFRACTION	f_plane_restr	0.0041	1816
X-RAY DIFFRACTION	f_dihedral_angle_d	10.481	3329

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 (%)
2.4-2.46	0.4233	130	0.3315	3785	X-RAY DIFFRACTION	92.47
2.46-2.52	0.3235	139	0.2782	4089	X-RAY DIFFRACTION	99.46
2.52-2.6	0.3295	144	0.2578	4129	X-RAY DIFFRACTION	99.4
2.6-2.68	0.3109	142	0.2625	4095	X-RAY DIFFRACTION	99.44
2.68-2.78	0.319	140	0.2584	4087	X-RAY DIFFRACTION	99.37
2.78-2.89	0.3011	141	0.2605	4102	X-RAY DIFFRACTION	99.32
2.89-3.02	0.3239	144	0.2641	4130	X-RAY DIFFRACTION	99.49
3.02-3.18	0.2822	142	0.2425	4123	X-RAY DIFFRACTION	99.88
3.18-3.38	0.2858	144	0.2364	4168	X-RAY DIFFRACTION	99.81
3.38-3.64	0.2866	144	0.2306	4138	X-RAY DIFFRACTION	99.72
3.64-4	0.2778	144	0.2105	4172	X-RAY DIFFRACTION	99.75
4-4.58	0.2366	144	0.197	4171	X-RAY DIFFRACTION	99.52
4.58-5.77	0.2048	145	0.1962	4228	X-RAY DIFFRACTION	99.75
5.77-38.9	0.2422	148	0.2077	4355	X-RAY DIFFRACTION	99.32

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	2.99616863418	-1.5023394336	1.45907538502	1.30870683069	-0.248794260506	5.23946586459	0.0205694508806	-0.0597239411637	0.508206163765	-0.497779925413	-0.0847901686136	-0.395284289707	-0.501001862257	0.55001733356	0.043924490784	0.788236599096	-0.178203713364	0.109229141431	0.454013884935	0.0342646000775	0.41005885744	-37.827	112.958	19.874
2	1.06871144541	0.354188934426	-0.0850991380899	1.67504623142	0.750784640357	1.81936614151	-0.138120684202	-0.259233082083	-0.0473602734444	0.0519473461909	0.0704171537054	0.0696317118074	0.129817086064	0.173685033248	0.0409979075297	0.478902939533	0.0102258307744	-0.00930449606463	0.503847582256	0.00987637678481	0.235042075951	-45.534	101.696	37.856
3	5.67132370099	-1.53632779185	0.419212972978	2.25623155189	0.195134637821	2.18655700677	-0.160391522044	0.0578598446964	-0.413997881991	0.250808962566	-0.0375723263685	0.0592100296292	0.364038958498	-0.0396459065431	0.244270772935	0.564751465714	0.0140819754446	-0.0433113798184	0.377984579261	-0.0187500027922	0.203450809975	-58.006	90.715	31.612
4	3.11665818872	0.232301636082	0.135066141839	1.09812345976	0.304082865915	1.41796210771	-0.0794676293806	-0.147307617062	0.107436623645	-0.0467234159421	-0.0170732241733	0.11489839229	-0.0561049150614	-0.151891940824	0.0961126424243	0.529298696012	0.0424870704738	-0.0366968930832	0.431529792202	-0.0216933408796	0.18511734922	-59.038	101.753	35.088
5	8.36477142769	1.95494756706	0.632594761901	1.39550853197	-1.94184106442	5.79967904294	0.249702517554	0.228336847179	1.22399264427	-0.123914976546	-0.566691137704	0.103116723008	-0.593750106781	-0.264159398813	0.250549855813	0.310831975758	-0.114776321581	0.0230973176015	0.446287251614	-0.0676929925267	0.289653089261	-40.098	113.999	33.64
6	2.97162990786	1.05883051073	-0.381143716724	5.53062651717	-0.840564695859	7.46858273117	0.839416948295	0.0234265536234	0.28025587796	-0.372792931117	1.16800185084	1.22930699086	-0.919658459359	-0.107791225922	-1.60212615469	1.02803535214	-0.0371558704302	0.0988462270026	0.427798256543	-0.0186882022803	1.10802209323	-54.874	132.696	25.141
7	7.60372120139	-2.24991569208	2.93463329788	5.42136203972	-3.98843248463	4.46035728263	-0.19081359647	0.256594574105	0.413857774328	1.23792168636	0.463687305971	1.09590053121	-1.13338141835	0.151924942531	-0.0495746870948	0.734980106302	-0.0162533823189	-0.112464120047	0.472362037281	0.118836219882	0.774231393605	-63.378	128.292	19.552
8	9.11064704775	-2.631090218	7.20593068882	1.37640732354	-2.17757588345	5.70912507255	-0.0988324333351	2.37919003326	0.131184905744	-1.26819645251	0.305473214799	0.2114381926	1.89373184664	0.479984687109	-0.0226177668566	1.29493809337	-0.221527234942	-0.201258453781	0.76191986755	0.192271182406	0.543451485745	-56.416	121.555	8.405
9	3.59111145002	-2.74844422751	1.85859872806	2.93146513272	-0.444952175499	3.17132940069	0.475566526488	0.301038692065	0.22504021613	-0.48331267919	-0.136018265953	0.14120929111	0.216642220543	0.150992093893	-0.330532521572	0.721398993532	-0.0883363220362	-0.0252142156337	0.438604792324	0.177521402469	0.539441003272	-56.267	126.532	14.816
10	0.767906165518	0.430906158491	0.613347538915	1.97972302338	-0.27881028755	1.60483824486	0.136438754365	0.409204920116	-1.25065960894	-0.03634829477	-0.102314717252	0.139988515016	0.333939561644	0.405694082186	-0.0245649172877	0.638072920911	0.0845164152843	0.033078124028	0.619972592534	-0.215155053808	1.64110767335	-41.43	35.245	20.539
11	2.64080571737	-0.267045397003	0.175064283235	1.20848387587	-0.246454037831	0.588517583588	-0.167659880482	0.548248505443	-1.31086116936	-0.263007903542	0.0838393699431	0.42668545007	0.100660510835	-0.0111586403802	0.0810489741813	0.644323874824	-0.0150764494239	0.056834842755	0.565761081774	-0.273753099977	1.4034019424	-58.718	43.783	14.041
12	1.33220754672	0.379577951372	0.628342692663	0.649221047046	-0.65906062593	1.37469461377	0.0805983995806	-0.192055048121	-0.832422835263	-0.0280246829872	0.352572310078	0.231373556635	0.555942877051	-0.333818836727	-0.317116646524	0.815349051867	0.0738087868631	0.0617014787859	0.702682623126	-0.0495788790808	2.53958052351	-54.431	18.797	27.295
13	1.04468920263	-0.365554071282	-0.221585269664	3.67559458397	1.18774013535	2.21038062326	0.235101269568	0.0432708070541	-0.0445843637879	0.133335921446	-0.033853881422	0.303994387206	-0.387318394958	-0.24333305844	-0.345411170303	0.825223935373	0.0345847287707	0.0967624932788	0.609245738187	0.273981313684	2.28061688867	-56.885	17.24	33.314
14	3.6708429296	-2.10660715745	1.29260440353	3.66497587209	-2.41010526789	4.7336306725	-0.00588614863532	-0.0943058823859	0.57772691068	-0.420155928857	-0.108549449211	-0.669980193143	-0.426481113607	0.908851680096	0.118412257823	0.506656331251	-0.120484302468	0.0944186438552	0.609135157971	-0.0884553074743	0.411078385924	-30.54	106.458	26.813
15	2.27063907963	0.509546242916	-0.146879767363	3.23675016004	0.931190549058	1.61808209193	0.0198641542732	0.225378588379	-0.2028381399	-0.405601646022	-0.0294738682204	-0.252277617893	0.0197563488094	0.117218612754	0.0163659357641	0.676067088306	0.0266026652946	0.0935454752735	0.482231596459	-0.0125318892285	0.23417402156	-41.516	87.631	12.912
16	4.10763335917	-0.990474719957	2.08051617168	4.27552921718	0.592500484803	4.85802049968	-0.152429295105	-0.383206366269	-0.526670925476	-0.258956779798	0.0864244231037	-0.85176190327	0.918845856674	1.11376708773	-0.0285825899344	0.470685769608	0.160879001703	0.145816322497	0.889651893891	0.112228272245	0.64297274846	-15.076	88.535	28.504
17	0.75583694669	0.956838200853	0.334070511872	2.77387242672	-2.01959325216	3.99700242061	-0.309875597219	0.0504625068528	-1.1470646065	-0.0354722030291	0.0141529540752	-0.0220955798572	0.42741044329	0.779622910088	0.234498183289	0.573898720497	0.107641055481	0.133230776381	0.653747134839	-0.103310795631	1.75366915533	-30.589	36.614	21.71
18	0.0082275730946	-0.0333282195376	0.000906173128145	0.865969961916	-0.285954434429	0.157812355693	-0.278517509074	-0.504089772303	-1.26317389638	0.428604781837	0.187054512884	0.167138785823	0.122199876042	0.034328811626	0.0961785481391	0.630849848753	0.161477697955	0.104580302508	0.508413740347	0.292770851694	1.24621006737	-41.589	46.559	38.419
19	4.4581141583	1.11501657467	0.191538865281	8.69038209448	0.912260629975	2.76157178638	-0.273155357227	0.0575353044107	-0.319179804825	-0.577451817429	0.0390102499817	0.443304783037	-0.576681485403	-0.0231044274985	0.250505381011	0.681664642716	0.0743968057521	-0.0673800275704	0.376218169069	0.053591319441	0.492754451848	-47.504	64.117	31.513
20	2.68656000692	1.22030465906	-1.84702728852	4.35922622221	-0.910919434772	2.54889313409	0.253061699465	-0.0437681291843	-0.160354133779	0.38450894891	-0.229714930272	-0.368554691642	-0.700334680832	0.0710421235078	-0.0427118330686	0.737700191421	0.0393995809218	-0.0770462946757	0.4293778881	0.116759330417	0.509832719611	-38.876	66.915	34.276
21	4.28059571661	-1.40250063511	-2.89015682872	5.32306376288	4.02005251812	4.32326363675	0.233923569317	-0.728554397202	0.0362217442128	-0.0202255973938	-0.0214319746987	-0.585947080225	-0.434825743895	0.233774499806	-0.209330110801	0.79831878214	0.0595676312098	-0.0579613838704	0.492166113915	0.223060353928	0.614165084595	-37.738	62.131	41.307
22	2.75706246833	0.421146379679	0.609854940487	3.72164690413	0.267514133413	3.4042108209	-0.214922994125	-0.186279597832	-1.08363126235	0.273419875156	0.198199101655	0.226579048554	-0.352971973213	0.0108823296404	0.0325592191903	0.543064968934	0.0662905436976	0.0342824882149	0.402441533615	0.159192810477	1.03750651453	-40.312	49.568	35.346
23	0.735094150831	2.31692201008	-0.45178091173	8.05055805801	1.24610808035	9.65905116305	0.531382967187	0.043068294307	-1.31801635617	-0.0453341066248	-0.554540767164	-0.939552310665	0.579392736786	1.18370435064	0.156451848318	0.677843576189	0.13467312248	0.0343721257028	0.37616409397	0.216261259217	1.53865378665	-29.703	39.292	35.513
24	1.81124316039	0.0588303510571	-0.109981244885	2.39576565167	-2.58073254218	3.10461840085	-0.321636717298	0.394233180467	-0.111174034088	0.5362987955	-0.486922453845	-0.645869623326	-1.80843742969	2.00142247607	0.829573739956	0.830379101435	-0.301894658943	-0.117819703808	1.3390859842	0.0479461305371	0.986456344678	-12.698	56.388	21.769
25	5.75678066634	0.223197724362	-0.763668450747	1.16291589361	-1.24580123138	7.88293302759	0.229632487912	0.890472143147	-0.655020137937	-0.0156176754987	0.0851720222869	-0.107103117707	-0.124064505209	0.22184953861	-0.232319846435	0.553995605813	-0.0437779838312	0.0392143043885	0.684579621999	-0.0072907360431	1.23262744635	-17.131	52.728	15.422

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 17:61 )	A	17 - 61
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 62:100 )	A	62 - 100
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 101:135 )	A	101 - 135
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 136:264 )	A	136 - 264
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 265:282 )	A	265 - 282
6	X-RAY DIFFRACTION	6	( CHAIN A AND RESID 283:302 )	A	283 - 302
7	X-RAY DIFFRACTION	7	( CHAIN A AND RESID 303:336 )	A	303 - 336
8	X-RAY DIFFRACTION	8	( CHAIN A AND RESID 337:354 )	A	337 - 354
9	X-RAY DIFFRACTION	9	( CHAIN A AND RESID 355:384 )	A	355 - 384
10	X-RAY DIFFRACTION	10	( CHAIN B AND RESID 17:100 )	B	17 - 100
11	X-RAY DIFFRACTION	11	( CHAIN B AND RESID 101:264 )	B	101 - 264
12	X-RAY DIFFRACTION	12	( CHAIN B AND RESID 265:354 )	B	265 - 354
13	X-RAY DIFFRACTION	13	( CHAIN B AND RESID 355:384 )	B	355 - 384
14	X-RAY DIFFRACTION	14	( CHAIN C AND RESID 17:61 )	C	17 - 61
15	X-RAY DIFFRACTION	15	( CHAIN C AND RESID 62:282 )	C	62 - 282
16	X-RAY DIFFRACTION	16	( CHAIN C AND RESID 283:383 )	C	283 - 383
17	X-RAY DIFFRACTION	17	( CHAIN D AND RESID 17:61 )	D	17 - 61
18	X-RAY DIFFRACTION	18	( CHAIN D AND RESID 62:100 )	D	62 - 100
19	X-RAY DIFFRACTION	19	( CHAIN D AND RESID 101:164 )	D	101 - 164
20	X-RAY DIFFRACTION	20	( CHAIN D AND RESID 165:188 )	D	165 - 188
21	X-RAY DIFFRACTION	21	( CHAIN D AND RESID 189:214 )	D	189 - 214
22	X-RAY DIFFRACTION	22	( CHAIN D AND RESID 215:264 )	D	215 - 264
23	X-RAY DIFFRACTION	23	( CHAIN D AND RESID 265:282 )	D	265 - 282
24	X-RAY DIFFRACTION	24	( CHAIN D AND RESID 283:344 )	D	283 - 344
25	X-RAY DIFFRACTION	25	( CHAIN D AND RESID 345:383 )	D	345 - 383

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