PDB-5has: Crystal structure of the N-terminal DCB-HUS domain of T. terrestr...

ID or keywords:

Entry

Database: PDB / ID: 5has

Title

Crystal structure of the N-terminal DCB-HUS domain of T. terrestris Sec7

Components

Sec7

Keywords

PROTEIN TRANSPORT / Armadillo / Arf-GEF / TGN / transport

Function / homology

Mon2/Sec7/BIG1-like, dimerisation and cyclophilin-binding domain / Mon2/Sec7/BIG1-like, dimerisation and cyclophilin-binding domain / Mon2/Sec7/BIG1-like, HUS domain / Mon2/Sec7/BIG1-like, HUS domain / protein transport / Golgi apparatus / Sec7

Function and homology information

Biological species

Thielavia terrestris (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.653 Å

Authors

Richardson, B.C. / Fromme, J.C.

Funding support

United States, 1items

Citation

Journal: Elife / Year: 2016
Title: The Sec7 N-terminal regulatory domains facilitate membrane-proximal activation of the Arf1 GTPase.
Authors: Richardson, B.C. / Halaby, S.L. / Gustafson, M.A. / Fromme, J.C.

History

Deposition	Dec 30, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 27, 2016	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2017	Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Dec 25, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Mar 6, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	5has_validation.pdf.gz	462.6 KB	Display	wwPDB validaton report
Full document	5has_full_validation.pdf.gz	482.3 KB	Display
Data in XML	5has_validation.xml.gz	47.1 KB	Display
Data in CIF	5has_validation.cif.gz	65.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ha/5has ftp://data.pdbj.org/pub/pdb/validation_reports/ha/5has	HTTPS FTP

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Related structure data

Similar structure data	3lkd-d 2akr-3 3bt2-2 1z5l-3 4eb2-1 7czf-2 4ygv-d 3gqa-d 2po6-1 3gq8-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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: Sec7

B: Sec7

C: Sec7

D: Sec7

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

1

A: Sec7

D: Sec7

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

2

B: Sec7

C: Sec7

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

3

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	62.472, 132.024, 247.664
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Sec7 Mass: 51893.070 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thielavia terrestris (fungus) / Gene: Sec7 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 / References: UniProt: A0A140UHP8*PLUS
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.4 Å³/Da / Density % sol: 48.86 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 5% Jeffamine ED2001, 150 mM MES pH 6, 6% DMSO

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

CHESS

/ Beamline: A1 / Wavelength: 0.987 Å

Detector

Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 14, 2013

Radiation

Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.987 Å / Relative weight: 1

Reflection

Redundancy: 10 % / Number: 482303 / R_merge(I) obs: 0.115 / Χ²: 0.85 / D res high: 2.85 Å / D res low: 50 Å / Num. obs: 48253 / % possible obs: 98.1

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	ID	R_merge(I) obs	Chi squared	Redundancy
7.73	50	1	0.07	1.113	10.9
6.14	7.73	1	0.073	0.849	11.5
5.36	6.14	1	0.091	0.856	11
4.87	5.36	1	0.089	0.996	10.6
4.52	4.87	1	0.089	1.018	10.4
4.26	4.52	1	0.096	1.013	10.2
4.04	4.26	1	0.11	1.082	10
3.87	4.04	1	0.134	1.173	9.9
3.72	3.87	1	0.154	1.076	9.8
3.59	3.72	1	0.184	0.994	9.6
3.48	3.59	1	0.233	0.879	9.7
3.38	3.48	1	0.29	0.768	9.4
3.29	3.38	1	0.361	0.706	9.6
3.21	3.29	1	0.477	0.669	9.5
3.14	3.21	1	0.603	0.639	9.7
3.07	3.14	1	0.755	0.634	9.5
3.01	3.07	1	0.911	0.621	9.6
2.95	3.01	1		0.604	9.6
2.9	2.95	1		0.585	9.5
2.85	2.9	1		0.569	9.6

Reflection

Resolution: 2.6→50 Å / Num. obs: 59678 / % possible obs: 99.3 % / Redundancy: 9.5 % / B_iso Wilson estimate: 65.16 Å² / R_merge(I) obs: 0.155 / Χ²: 1.035 / Net I/av σ(I): 12.098 / Net I/σ(I): 10.6 / Num. measured all: 569136

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Redundancy (%)	Num. unique all	Χ²	% possible all	R_merge(I) obs
2.6-2.64	4.7	2714	0.821	91.3
2.64-2.69	5.9	2884	0.824	97.3
2.69-2.74	7.2	2924	0.857	99.5
2.74-2.8	7.9	2977	0.892	100	0.987
2.8-2.86	8.6	2943	0.919	99.9	0.897
2.86-2.93	9.1	2954	0.935	99.8	0.849
2.93-3	9.5	2947	0.992	99.8	0.741
3-3.08	9.6	2989	1.074	99.9	0.595
3.08-3.17	9.7	2951	1.152	99.9	0.452
3.17-3.28	9.7	2965	1.254	99.9	0.352
3.28-3.39	9.7	3002	1.273	99.9	0.278
3.39-3.53	9.7	2953	1.171	100	0.236
3.53-3.69	9.7	2995	1.161	100	0.197
3.69-3.88	9.8	2995	1.137	100	0.177
3.88-4.13	10	3014	0.998	100	0.156
4.13-4.45	10.3	3018	1.032	100	0.139
4.45-4.89	11	3024	0.974	100	0.13
4.89-5.6	11.9	3076	1.014	100	0.124
5.6-7.05	13.1	3085	0.984	100	0.12
7.05-50	12.4	3268	0.972	99.7	0.115

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Phasing

Phasing	Method: SAD

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
SCALEPACK		data scaling
PHASER		phasing
PHENIX	1.8.2_1309	refinement
PDB_EXTRACT	3.15	data extraction
HKL-2000		data reduction

Refinement

Method to determine structure:

SAD / Resolution: 2.653→31.184 Å / FOM work R set: 0.7911 / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.43 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2568	2476	4.16 %
R_work	0.2119	56990	-
obs	0.2137	59466	98.59 %

Solvent computation

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

Displacement parameters

B_iso max: 209.25 Å² / B_iso mean: 89.68 Å² / B_iso min: 23.36 Å²

Refinement step

Cycle: final / Resolution: 2.653→31.184 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10887	0	0	57	10944
B_iso mean	-	-	-	60.27	-
Num. residues	-	-	-	-	1383

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	11038
X-RAY DIFFRACTION	f_angle_d	1.232	14907
X-RAY DIFFRACTION	f_chiral_restr	0.083	1815
X-RAY DIFFRACTION	f_plane_restr	0.006	1859
X-RAY DIFFRACTION	f_dihedral_angle_d	12.637	4123

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / 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 (%)
2.6535-2.7045	0.408	119	0.3206	2586	2705	81
2.7045-2.7597	0.3158	131	0.2986	3054	3185	97
2.7597-2.8196	0.3305	138	0.2778	3157	3295	100
2.8196-2.8852	0.3399	134	0.2664	3147	3281	100
2.8852-2.9573	0.3186	137	0.265	3182	3319	100
2.9573-3.0372	0.2928	138	0.2549	3155	3293	100
3.0372-3.1265	0.3024	137	0.2445	3184	3321	100
3.1265-3.2273	0.2955	138	0.2322	3174	3312	100
3.2273-3.3425	0.2715	137	0.235	3163	3300	100
3.3425-3.4762	0.3004	139	0.2211	3206	3345	100
3.4762-3.6341	0.2369	137	0.2147	3176	3313	100
3.6341-3.8254	0.2448	140	0.2021	3197	3337	100
3.8254-4.0646	0.2225	136	0.1956	3193	3329	100
4.0646-4.3777	0.2232	141	0.1794	3216	3357	100
4.3777-4.8168	0.2008	141	0.1609	3224	3365	100
4.8168-5.5104	0.2376	141	0.1948	3252	3393	100
5.5104-6.93	0.3057	144	0.253	3309	3453	100
6.93-31.1861	0.2426	148	0.1971	3415	3563	99

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	2.6203	1.6247	-3.4325	7.8025	0.7551	8.8829	0.2857	0.731	0.8888	-0.4594	0.0996	-0.3274	-0.9918	0.1359	-0.3072	0.6111	-0.0643	-0.0139	0.6106	0.1502	0.5376	41.1253	103.6447	100.02
2	9.5644	0.3102	5.2089	1.4724	1.203	2.234	0.0112	0.3257	-0.467	0.0547	0.2793	-0.1738	-0.0544	0.1541	-0.2844	0.343	-0.0225	0.0203	0.3791	0.0869	0.4455	49.3465	97.8166	111.2958
3	5.023	1.6222	-0.0495	5.1135	-0.5747	5.8132	0.1969	0.084	0.5213	-0.0883	-0.0543	-0.1335	-0.214	0.1246	-0.1283	0.2155	-0.033	0.0075	0.239	0.0608	0.3821	34.8535	92.5006	116.4457
4	3.44	-3.202	5.6845	5.1886	-3.6471	8.4196	0.4478	0.2284	-0.324	-0.1967	-0.3497	-0.4537	0.6842	0.5884	-0.2525	0.3126	0.0226	-0.0163	0.2658	0.0421	0.5666	42.6643	77.993	123.3714
5	3.1641	0.2057	-1.4791	4.87	-0.5836	5.3219	0.3182	-0.3592	0.3643	0.3043	-0.0985	-0.4102	-0.2541	0.542	-0.2661	0.3213	-0.0234	-0.0879	0.3353	0.0275	0.4544	41.7132	85.4699	134.6462
6	3.72	-0.7358	-0.0577	3.4851	-0.9161	4.2995	-0.024	-0.3421	-0.2049	0.2	0.03	0.0653	0.1542	0.1592	0.0089	0.3621	0.008	0.0032	0.2862	0.054	0.4261	35.0499	77.083	137.2258
7	4.838	2.0089	2.3684	8.4753	1.5666	6.5056	-0.3166	-0.473	-0.6764	0.2827	0.0851	0.2173	-0.0513	-0.1098	0.2256	0.4065	-0.0406	0.1767	0.4316	0.1495	0.5378	23.2741	66.3816	144.6224
8	2.7713	0.1282	-0.4318	6.9156	1.1237	2.9483	0.2889	-1.4921	-0.8476	1.7263	0.0339	-0.8784	0.6105	-0.3171	-0.2969	1.3461	0.1836	-0.2376	1.5437	0.4631	1.0215	54.8526	28.484	158.8925
9	5.1382	-1.6857	-0.2577	3.5694	-0.111	4.0512	-0.2583	-0.6084	-1.0937	0.9888	0.2691	0.1139	0.6213	0.1776	-0.0273	0.725	0.072	0.079	0.4006	0.125	0.6371	45.1904	36.8657	143.5261
10	2.9756	0.7134	1.5289	4.5988	-2.2451	2.9853	0.0912	0.38	0.7664	0.2121	-0.2741	-0.5694	-0.2672	0.6136	0.1553	0.5194	0.0717	0.1279	0.4428	0.0804	0.9377	57.0141	59.3841	126.7026
11	5.9494	-1.8887	3.4195	3.3678	-1.3343	4.5112	0.3458	0.8544	-0.3283	-0.2665	-0.2906	-0.6657	0.5065	0.8157	-0.1093	0.4482	0.05	0.1728	0.4521	0.0201	0.7159	49.648	45.783	122.3091
12	7.5226	1.6995	1.3828	2.3088	2.5926	6.3076	0.3058	-0.6892	-1.4226	-0.0488	-0.5376	1.358	0.0869	-1.1661	0.2649	0.6508	-0.0389	0.125	0.5345	0.0119	1.2949	24.5352	41.4348	127.1141
13	4.0984	0.7563	1.7329	4.2131	-0.2427	3.9194	-0.2115	0.3238	0.1002	-0.2385	0.0542	-0.1847	0.1194	0.2195	0.1563	0.3769	0.0083	0.1251	0.2674	0.013	0.4913	39.3121	53.764	119.0958
14	4.8825	-5.0578	-2.7021	6.0567	0.2516	7.97	-0.3133	0.1605	0.0324	-0.33	0.2665	0.6259	0.2754	-0.6526	0.087	0.292	-0.0909	-0.0934	0.3867	0.0679	0.5438	22.9628	59.8184	114.1094
15	0.7264	0.9591	0.1377	0.9707	0.1587	-0.0038	-0.5032	0.3467	1.6055	-0.7947	-0.0721	0.0758	-0.7043	-0.0783	0.4204	1.4888	1.1603	-0.4814	2.5741	0.2092	1.8624	-8.0824	105.262	68.2755
16	2.6996	0.8187	-0.7334	1.8241	0.7602	1.4044	0.2061	-0.6529	-0.4679	-0.3262	-0.1982	0.3572	-1.2418	-0.8699	-0.0195	1.6532	0.2456	-0.4837	1.6846	0.2664	1.3321	-5.8901	98.8078	66.0513
17	2.3395	0.9356	1.4804	3.0431	1.35	3.8971	0.4168	0.2759	-0.094	0.1504	0.0341	-0.0986	0.3487	-0.4433	-0.4833	1.3314	0.2453	-0.3249	1.4657	0.2819	1.0918	1.6444	94.6604	77.8473
18	1.6621	-2.0308	0.1513	3.0705	-2.1023	1.3849	0.2859	0.2688	-0.4985	-1.2348	0.0127	0.9637	0.5903	-0.47	-0.1398	1.199	-0.0324	-0.5076	1.1907	-0.0881	0.9746	10.4216	80.3677	86.8949
19	7.8628	-2.9687	-2.3438	5.2573	-2.2905	2.9648	0.3302	1.6802	0.4139	-1.2303	0.18	0.597	0.5376	-0.5158	-0.5646	1.2007	-0.0815	-0.2149	1.073	-0.0852	0.6395	15.8512	78.6409	86.0757
20	4.9291	2.2006	0.9921	7.7362	0.4388	4.9486	-0.1469	0.7639	0.0895	-1.2874	0.0735	1.2692	0.4913	-0.3069	0.1421	0.7622	-0.0906	-0.2788	0.922	0.04	0.6761	12.3985	74.6631	91.4623
21	4.9216	-1.6154	-0.0732	8.3782	-2.81	10.0792	0.0018	0.6296	-0.6391	-0.7549	0.055	0.1087	0.908	-0.0703	-0.0394	0.3612	-0.0614	-0.0465	0.3937	-0.0726	0.4711	21.2422	69.6097	102.1834
22	0.0182	-0.0846	-0.0089	0.1183	0.0285	-0.0135	-0.2884	-0.6652	-0.4981	0.504	0.0164	-0.1287	-0.1374	-0.2184	0.2222	2.1261	-1.0093	0.7185	1.0521	-0.0761	1.3333	6.2162	19.638	194.7716
23	7.0586	-0.7865	-3.437	0.2671	1.1154	4.8117	0.0305	-1.6509	-0.0859	1.5042	0.4876	0.4716	0.1601	0.399	-0.3071	1.8835	-0.2429	0.5625	1.6054	0.6375	1.2186	6.5111	26.4902	200.4274
24	2.7044	0.9068	-0.2791	3.1965	-2.1802	5.6967	-0.1583	-0.5317	-0.9412	-0.1274	-0.0964	-0.0797	1.3268	-0.3832	0.2127	1.4317	-0.0031	0.4484	0.8256	0.1992	0.9779	14.078	34.1152	181.7344
25	1.8201	2.5767	-1.5713	4.702	-2.0981	4.371	0.2315	-1.976	0.0221	0.9241	-0.3398	0.5554	-0.6076	-0.1599	0.0654	1.2078	0.2291	0.1723	1.1928	0.0851	0.8862	16.4876	61.5981	175.655
26	4.8157	1.34	-1.0329	0.7126	0.3868	2.2624	0.5014	-1.8849	0.3424	1.7188	-0.4423	2.1982	-0.731	-0.3786	0.0637	1.4015	0.0538	2.5071	1.7868	0.4814	-0.6607	4.8067	54.6453	186.5551
27	6.2983	0.1029	-1.335	4.5866	-1.0917	6.6233	-0.2235	-0.601	-0.2284	0.8963	0.3437	0.2704	-0.0816	-0.2228	-0.104	0.8933	0.1819	0.1756	0.6223	0.1699	0.5091	20.1904	49.4266	169.8012
28	2.9021	0.4411	-1.0461	5.3969	-1.1325	8.194	-0.0459	-0.4898	0.211	0.8899	-0.0478	0.1125	-0.334	-0.3035	0.0696	0.6297	0.0702	0.1572	0.4892	0.0898	0.5586	23.6311	58.4664	160.6914

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 4:62)	A	4 - 62
2	X-RAY DIFFRACTION	2	(chain A and resid 63:97)	A	63 - 97
3	X-RAY DIFFRACTION	3	(chain A and resid 98:156)	A	98 - 156
4	X-RAY DIFFRACTION	4	(chain A and resid 157:195)	A	157 - 195
5	X-RAY DIFFRACTION	5	(chain A and resid 196:333)	A	196 - 333
6	X-RAY DIFFRACTION	6	(chain A and resid 334:420)	A	334 - 420
7	X-RAY DIFFRACTION	7	(chain A and resid 421:458)	A	421 - 458
8	X-RAY DIFFRACTION	8	(chain B and resid 5:46)	B	5 - 46
9	X-RAY DIFFRACTION	9	(chain B and resid 47:170)	B	47 - 170
10	X-RAY DIFFRACTION	10	(chain B and resid 171:244)	B	171 - 244
11	X-RAY DIFFRACTION	11	(chain B and resid 245:320)	B	245 - 320
12	X-RAY DIFFRACTION	12	(chain B and resid 321:345)	B	321 - 345
13	X-RAY DIFFRACTION	13	(chain B and resid 346:420)	B	346 - 420
14	X-RAY DIFFRACTION	14	(chain B and resid 421:458)	B	421 - 458
15	X-RAY DIFFRACTION	15	(chain C and resid 7:28)	C	7 - 28
16	X-RAY DIFFRACTION	16	(chain C and resid 29:59)	C	29 - 59
17	X-RAY DIFFRACTION	17	(chain C and resid 60:141)	C	60 - 141
18	X-RAY DIFFRACTION	18	(chain C and resid 142:304)	C	142 - 304
19	X-RAY DIFFRACTION	19	(chain C and resid 305:333)	C	305 - 333
20	X-RAY DIFFRACTION	20	(chain C and resid 334:382)	C	334 - 382
21	X-RAY DIFFRACTION	21	(chain C and resid 383:457)	C	383 - 457
22	X-RAY DIFFRACTION	22	(chain D and resid 7:26)	D	7 - 26
23	X-RAY DIFFRACTION	23	(chain D and resid 27:53)	D	27 - 53
24	X-RAY DIFFRACTION	24	(chain D and resid 54:180)	D	54 - 180
25	X-RAY DIFFRACTION	25	(chain D and resid 181:263)	D	181 - 263
26	X-RAY DIFFRACTION	26	(chain D and resid 264:307)	D	264 - 307
27	X-RAY DIFFRACTION	27	(chain D and resid 308:365)	D	308 - 365
28	X-RAY DIFFRACTION	28	(chain D and resid 366:457)	D	366 - 457

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