PDB-7yh3: TRAPPC3 from Thorarchaeota SMTZ1-45

ID or keywords:

Entry

Database: PDB / ID: 7yh3

Title

TRAPPC3 from Thorarchaeota SMTZ1-45

Components

TRAPPC3 from Thorarchaeota SMTZ1-45

Keywords

UNKNOWN FUNCTION / Asgard archaea / TRAPP

Function / homology

Transport protein particle (TRAPP) component / Transport protein particle (TRAPP) component / NO signalling/Golgi transport ligand-binding domain superfamily / 4-vinyl reductase 4VR domain-containing protein

Function and homology information

Biological species

Candidatus Thorarchaeota archaeon SMTZ1-45 (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Robinson, R.C. / Tran, L.T.

Funding support

Japan, 3items

Citation

Journal: To Be Published
Title: TRAPPC3 from Thorarchaeota SMTZ1-45
Authors: Tran, L.T. / Robinson, R.C.

History

Deposition	Jul 12, 2022	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 19, 2023	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7yh3.cif.gz	275.6 KB	Display	PDBx/mmCIF format
PDB format	pdb7yh3.ent.gz	221.8 KB	Display	PDB format
PDBx/mmJSON format	7yh3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7yh3_validation.pdf.gz	2.9 MB	Display	wwPDB validaton report
Full document	7yh3_full_validation.pdf.gz	2.9 MB	Display
Data in XML	7yh3_validation.xml.gz	34.1 KB	Display
Data in CIF	7yh3_validation.cif.gz	49.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yh/7yh3 ftp://data.pdbj.org/pub/pdb/validation_reports/yh/7yh3	HTTPS FTP

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Related structure data

Related structure data	7yh2S S: Starting model for refinement
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	#133 - Jan 2011 Nitric Oxide Synthase similarity (1)

Deposited unit

A: TRAPPC3 from Thorarchaeota SMTZ1-45

B: TRAPPC3 from Thorarchaeota SMTZ1-45

C: TRAPPC3 from Thorarchaeota SMTZ1-45

D: TRAPPC3 from Thorarchaeota SMTZ1-45

hetero molecules

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

1

A: TRAPPC3 from Thorarchaeota SMTZ1-45

C: TRAPPC3 from Thorarchaeota SMTZ1-45

hetero molecules

defined by author&software
36.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: TRAPPC3 from Thorarchaeota SMTZ1-45

D: TRAPPC3 from Thorarchaeota SMTZ1-45

hetero molecules

defined by author&software
Evidence: homology
36.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	68.387, 62.060, 69.324
Angle α, β, γ (deg.)	90.000, 100.460, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	TRAPPC3 from Thorarchaeota SMTZ1-45 Mass: 18089.672 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candidatus Thorarchaeota archaeon SMTZ1-45 (archaea) Gene: AM325_04720 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A135VRB8
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 710 / 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 Å³/Da / Density % sol: 38.48 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 00 mM HEPES pH 7.5 250 mM Mg(HCO2)2 18% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
Detector	Type: RAYONIX MX300-HS / Detector: CCD / Date: Apr 6, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.7→20 Å / Num. obs: 51122 / % possible obs: 94.9 % / Redundancy: 3.8 % / R_merge(I) obs: 0.048 / R_pim(I) all: 0.028 / R_rim(I) all: 0.056 / Net I/σ(I): 22.9
Reflection shell	Resolution: 1.7→1.73 Å / R_merge(I) obs: 0.351 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2550 / CC_1/2: 0.932 / R_pim(I) all: 0.177 / R_rim(I) all: 0.351

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Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
PDB_EXTRACT	3.27	data extraction
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7YH2

7yh2

Resolution: 1.7→19.48 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.38 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2584	2486	4.86 %
R_work	0.2164	48636	-
obs	0.2185	51122	81.31 %

Solvent computation

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

Displacement parameters

B_iso max: 93.8 Å² / B_iso mean: 26.2237 Å² / B_iso min: 4.02 Å²

Refinement step

Cycle: final / Resolution: 1.7→19.48 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4928	0	4	710	5642
B_iso mean	-	-	11.5	33.79	-
Num. residues	-	-	-	-	616

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 18

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.7-1.73	0.3614	76	0.2909	1270	1346	39
1.73-1.77	0.3203	75	0.2796	1469	1544	45
1.77-1.81	0.2876	80	0.2682	1658	1738	50
1.81-1.85	0.3397	98	0.2573	1892	1990	57
1.85-1.89	0.3246	117	0.2567	2136	2253	64
1.89-1.95	0.2699	125	0.261	2345	2470	71
1.95-2	0.2903	118	0.2595	2594	2712	78
2-2.07	0.2845	142	0.2532	2808	2950	85
2.07-2.14	0.2729	159	0.2478	3062	3221	93
2.14-2.23	0.3157	157	0.2336	3199	3356	97
2.23-2.33	0.2565	135	0.2394	3267	3402	98
2.33-2.45	0.2912	175	0.2252	3277	3452	98
2.45-2.6	0.2686	184	0.2214	3198	3382	98
2.6-2.8	0.2497	168	0.2199	3280	3448	99
2.8-3.09	0.2477	154	0.2139	3298	3452	98
3.09-3.53	0.2331	162	0.1885	3291	3453	99
3.53-4.44	0.2153	196	0.1679	3302	3498	99
4.44-19.48	0.2357	165	0.1932	3290	3455	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	0.5481	0.2748	-0.1117	0.3616	0.1933	0.6623	0.0169	-0.0541	-0.1568	0.044	-0.0072	-0.008	0.0735	-0.0244	-0.0483	0.0388	0.0054	-0.0312	0.1131	-0.0657	0.1275	-5.408	-0.5886	17.0973
2	1.0058	-0.0897	-0.0474	0.1768	0.2027	0.425	-0.0496	0.1237	0.2898	0.0168	0.1197	-0.0417	-0.043	0.1287	0.7734	0.0674	0.0151	-0.0643	0.1178	-0.0101	0.2091	-5.2191	3.9331	5.0999
3	0.3224	-0.3341	-0.0709	0.3981	0.369	1.7054	0.0523	0.0119	0.0907	-0.0336	0.0914	-0.2147	-0.154	0.3718	0.2111	0.1342	0.0386	-0.0001	0.2514	0.044	0.3067	12.7518	4.5751	0.0734
4	0.333	0.5712	-0.1573	0.9803	-0.27	0.0744	0.0421	0.3614	0.0004	-0.401	0.0145	-0.0407	0.2148	0.1302	0.0575	0.3152	0.1546	0.0602	0.4676	0.1024	0.2074	10.4828	-7.6362	-3.2565
5	0.0913	-0.1504	0.088	0.2471	-0.1445	0.0843	0.0314	-0.0827	-0.1397	0.0555	-0.042	-0.1387	0.0533	0.1089	-0.3026	0.0715	0.0615	-0.041	0.2205	0.0296	0.1261	5.3228	-5.065	16.527
6	1.1269	0.0281	-0.4362	0.462	-0.2491	1.4646	-0.0516	0.133	-0.0612	-0.0844	-0.0754	0.0072	0.1345	0.0902	-1.1568	0.0614	0.0319	-0.0368	0.0961	-0.0277	0.0955	-0.0342	-2.1058	3.4946
7	0.1686	-0.0505	-0.1082	0.0807	0.083	0.1082	0.015	0.0425	-0.055	-0.0503	-0.0488	0.0535	0.0417	0.0183	0.0053	0.1753	0.0933	0.0442	0.1123	0.0217	0.0963	4.209	-7.8817	4.2797
8	0.6905	0.1313	0.2796	0.5411	-0.0152	0.6764	-0.0914	0.0833	0.2014	0.0626	0.0395	0.0034	-0.1744	-0.0218	0.0888	0.093	0.0224	0.0028	0.0463	0.0597	0.087	33.3196	40.5405	17.8618
9	0.242	0.0334	-0.0857	0.3492	-0.1559	0.9014	0.0273	0.0936	-0.1233	-0.056	-0.0721	-0.2096	0.3307	0.1553	-0.059	0.1739	0.0155	0.0213	0.1165	0.0287	0.1038	36.8828	35.0995	6.6711
10	0.5649	-0.2905	-0.8868	0.1895	0.5007	1.4434	0.0063	0.1649	-0.0711	-0.0104	-0.1133	0.0609	0.1057	-0.0639	-0.4766	0.2345	0.0116	-0.0975	0.1789	0.089	0.263	22.9547	32.6363	-5.2603
11	0.8292	-0.1806	-0.1215	0.4615	0.4167	1.1416	0.0396	0.2454	0.0442	-0.1417	0.0161	0.0546	-0.3682	-0.1519	0.1648	0.149	0.0229	-0.0025	0.1217	0.0444	0.0829	28.9034	44.5409	2.7624
12	0.9241	-0.3246	-0.0794	0.2692	0.1602	0.3039	-0.0219	-0.0788	0.2225	-0.0347	-0.0666	0.0985	-0.0385	-0.1	-0.2266	0.0549	0.0271	-0.0181	0.1229	-0.1074	0.1572	-4.289	12.5512	15.116
13	0.0458	-0.0226	-0.0273	0.0735	0.0402	0.0279	0.0107	-0.0164	0.0409	0.0227	-0.068	0.1269	-0.0082	-0.0686	-0.0626	0.1098	-0.0462	0.0828	0.2342	-0.1735	0.3194	-12.7503	9.7428	25.6592
14	0.0055	0.0012	-0.0018	0.0026	-0.0019	0.0016	-0.035	0.052	-0.032	-0.0278	-0.05	-0.0337	0.0044	0.0118	-0.0002	0.6942	0.0492	0.1171	0.5908	-0.0656	0.6384	6.2756	-0.4086	32.9845
15	1.1188	-0.8219	-1.1382	0.6763	0.8226	1.1609	-0.0839	-0.4085	-0.1266	0.3442	-0.0436	-0.0366	0.2226	0.031	-0.287	0.2804	-0.1056	-0.0462	0.288	-0.0217	0.1686	4.8463	9.4722	39.9513
16	0.0763	-0.1215	-0.0365	0.3124	0.1277	0.0581	-0.0231	-0.0444	0.0075	0.1343	0.0299	0.0296	0.0261	0.0664	-0.1135	0.1465	-0.0619	0.0591	0.2044	-0.0937	0.1298	1.689	20.6505	37.893
17	2.3981	0.1134	-0.0302	0.2779	0.3762	1.2078	0.1023	0.1444	0.2275	-0.0225	-0.1987	0.2081	-0.1457	-0.2509	-0.7243	0.0697	0.0037	0.0348	0.1724	-0.0956	0.1621	-4.288	21.7596	20.4308
18	3.2776	-0.0823	-0.5208	1.6127	1.5371	1.525	-0.0262	-0.3946	-0.2649	0.3478	-0.1365	0.1603	0.3219	-0.0719	0.2509	0.1585	-0.0786	0.0884	0.1845	-0.0585	0.1555	-4.4835	8.256	33.9242
19	0.0941	-0.0989	0.0333	0.6543	0.0397	0.022	0.0098	-0.0562	-0.0478	0.2376	-0.1072	0.2075	0.0862	-0.1736	-0.7486	0.1701	-0.0816	0.0945	0.2141	-0.1381	0.1966	-5.8805	19.4111	33.1185
20	1.8206	1.0312	0.7059	1.2445	0.5862	0.8046	0.0596	0.0973	-0.1847	-0.0162	0.0139	-0.1852	0.246	0.108	0.3346	0.2603	0.0432	0.0711	0.0727	0.0093	0.0987	34.2065	26.3612	16.1997
21	0.6172	-0.657	0.5133	0.7999	-0.5231	0.4489	-0.1284	-0.0363	0.0466	0.051	-0.0708	-0.3063	0.0289	0.1425	-0.3982	0.1237	0.0449	0.0508	0.0691	0.0491	0.1691	35.1309	30.9773	29.0724
22	0.2033	0.26	0.0234	0.5867	0.4669	1.5669	-0.0633	0.0562	0.078	-0.2847	-0.0848	0.1089	0.0761	-0.2988	-0.8361	0.2434	0.0126	-0.0192	0.0918	0.0125	0.1601	20.9733	25.2876	30.0905
23	0.2587	-0.1005	-0.055	0.1146	0.0779	0.1961	0.0125	-0.0071	0.0118	0.012	0.0384	0.002	0.0152	-0.0272	0.6642	0.0465	0.0148	-0.0328	0.0397	0.012	0.0699	27.1403	31.479	32.9021
24	0.1519	0.1403	-0.0527	0.394	-0.1059	0.1539	-0.0422	0.0755	0.0052	-0.2219	-0.0092	-0.1111	0.1489	-0.0045	-0.2708	0.233	-0.0277	0.0253	0.0526	0.0021	0.1087	27.5629	20.9471	32.9723

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 3 through 26 )	A	3 - 26
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 27 through 47 )	A	27 - 47
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 48 through 85 )	A	48 - 85
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 86 through 97 )	A	86 - 97
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 98 through 107 )	A	98 - 107
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 108 through 141 )	A	108 - 141
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 142 through 157 )	A	142 - 157
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 3 through 26 )	B	3 - 26
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 27 through 48 )	B	27 - 48
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 49 through 77 )	B	49 - 77
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 78 through 157 )	B	78 - 157
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 3 through 22 )	C	3 - 22
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 23 through 45 )	C	23 - 45
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 46 through 54 )	C	46 - 54
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 55 through 77 )	C	55 - 77
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 78 through 97 )	C	78 - 97
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 98 through 117 )	C	98 - 117
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 118 through 131 )	C	118 - 131
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 132 through 157 )	C	132 - 157
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 1 through 26 )	D	1 - 26
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 27 through 45 )	D	27 - 45
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 46 through 117 )	D	46 - 117
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 118 through 130 )	D	118 - 130
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 131 through 157 )	D	131 - 157

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