PDB-4kv2: Ubiquitin-like domain of the mycobacterium tuberculosis type VII ...

ID or keywords:

Entry

Database: PDB / ID: 4kv2

Title

Ubiquitin-like domain of the mycobacterium tuberculosis type VII secretion system protein ECCD1

Components

ESX-1 secretion system protein eccD1

Keywords

PROTEIN TRANSPORT / ESX-1 / ESX / snm4 / ubiquitin / YukD / PF08817 / membrane protein / protein secretion

Function / homology

Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Roll / Alpha Beta / :

Function and homology information

Biological species

Mycobacterium tuberculosis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.88 Å

Authors

Korotkov, K.V. / Evans, T.J.

Citation

Journal: Bmc Struct.Biol. / Year: 2016
Title: Structures of EccB1 and EccD1 from the core complex of the mycobacterial ESX-1 type VII secretion system.
Authors: Wagner, J.M. / Chan, S. / Evans, T.J. / Kahng, S. / Kim, J. / Arbing, M.A. / Eisenberg, D. / Korotkov, K.V.

History

Deposition	May 22, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 9, 2014	Provider: repository / Type: Initial release
Revision 1.1	Mar 23, 2016	Group: Database references
Revision 1.2	Sep 20, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4kv2.cif.gz	85 KB	Display	PDBx/mmCIF format
PDB format	pdb4kv2.ent.gz	65.6 KB	Display	PDB format
PDBx/mmJSON format	4kv2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4kv2_validation.pdf.gz	414.9 KB	Display	wwPDB validaton report
Full document	4kv2_full_validation.pdf.gz	414.9 KB	Display
Data in XML	4kv2_validation.xml.gz	10.4 KB	Display
Data in CIF	4kv2_validation.cif.gz	14.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kv/4kv2 ftp://data.pdbj.org/pub/pdb/validation_reports/kv/4kv2	HTTPS FTP

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Related structure data

Related structure data	4kk7C 4kv3SC 5cyuC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2b6m-1 6n90-d 1ti1-d 1v7r-d 5com-2 2yjc-d 5qky-1 5qkq-1 6pc9-1 1bol-d Search similar-shape structures by Omokage search (details) 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	#60 - Dec 2004 Ubiquitin similarity (1)

Deposited unit

A: ESX-1 secretion system protein eccD1

B: ESX-1 secretion system protein eccD1

19.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	46.720, 46.720, 279.020
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	179
Space group name H-M	P6₅22

#1: Protein	ESX-1 secretion system protein eccD1 Mass: 9625.893 Da / Num. of mol.: 2 / Fragment: UNP residues 21-109 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv3877, RVBD_3877 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: I6X8K0
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

ESX-1 secretion system protein eccD1

Mass: 9625.893 Da / Num. of mol.: 2 / Fragment: UNP residues 21-109
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv3877, RVBD_3877 / Production host:

Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: I6X8K0

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.28 Å³/Da / Density % sol: 46.12 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1M TRIS-HCL PH 8.5, 0.2M MAGNESIUM CHLORIDE, 30% PEG4000, vapor diffusion, sitting drop, temperature 295K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 22-ID / Wavelength: 1 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 13, 2012

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.88→46.5 Å / Num. obs: 15843 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 13.4 % / B_iso Wilson estimate: 30.083 Å² / R_merge(I) obs: 0.106 / Net I/σ(I): 20.64

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Highest resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. unique obs	% possible all
1.88-1.93		13.9	0.996	3.07	15768	1136	100
1.93-1.98			0.747	3.96	15176	1083	99.9
1.98-2.04			0.643	4.58	15141	1083	100
2.04-2.1			0.517	5.78	14470	1037	100
2.1-2.17			0.403	7.5	14080	1015	100
2.17-2.25			0.351	8.48	13935	1001	100
2.25-2.33			0.271	11.04	13307	960	100
2.33-2.43			0.223	13.2	12464	903	100
2.43-2.54			0.175	16.37	12201	888	100
2.54-2.66			0.147	19.19	11509	839	100
2.66-2.8			0.125	22.29	11322	830	100
2.8-2.97			0.098	26.87	10328	781	100
2.97-3.18			0.08	32.15	9757	734	100
3.18-3.43			0.061	39.64	8978	700	100
3.43-3.76			0.055	43.56	8074	636	100
3.76-4.2			0.041	50.69	7372	599	100
4.2-4.85			0.035	57.87	6405	527	100
4.85-5.95			0.036	54.84	5668	474	100
5.95-8.41			0.036	52	4316	375	100
	8.41		0.026	58.53	2280	242	98.8

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHASER		phasing
REFMAC		refinement
PDB_EXTRACT	3.11	data extraction
SERGUI		data collection
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 4KV3

4kv3

Resolution: 1.88→46.5 Å / Cor.coef. F_o:F_c: 0.954 / Cor.coef. F_o:F_c free: 0.928 / WR_factor R_free: 0.215 / WR_factor R_work: 0.1741 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8791 / SU B: 5.887 / SU ML: 0.096 / SU R Cruickshank DPI: 0.1485 / SU R_free: 0.1436 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2358	794	5 %	RANDOM
R_work	0.1879	-	-	-
obs	0.1902	15842	99.97 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso max: 99.71 Å² / B_iso mean: 29.184 Å² / B_iso min: 11.16 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.34 Å²	-0.34 Å²	0 Å²
2-	-	-0.34 Å²	0 Å²
3-	-	-	1.11 Å²

Refinement step

Cycle: LAST / Resolution: 1.88→46.5 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1332	0	0	186	1518

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.02	1363
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1320
X-RAY DIFFRACTION	r_angle_refined_deg	1.331	2.001	1871
X-RAY DIFFRACTION	r_angle_other_deg	0.738	3	3041
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.603	5	180
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	23.906	24.286	49
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.031	15	211
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	10.214	15	9
X-RAY DIFFRACTION	r_chiral_restr	0.072	0.2	237
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	1524
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	261
X-RAY DIFFRACTION	r_mcbond_it	0.42	0.942	720
X-RAY DIFFRACTION	r_mcbond_other	0.42	0.941	719
X-RAY DIFFRACTION	r_mcangle_it	0.698	1.411	897

LS refinement shell

Resolution: 1.88→1.929 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.252	60	-
R_work	0.221	1071	-
all	-	1131	-
obs	-	-	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	3.815	-1.6155	-1.5155	15.2598	3.9919	4.9385	-0.0016	-0.0109	0.0254	0.5802	-0.0519	-0.2895	0.2766	-0.1576	0.0536	0.1437	-0.0751	-0.0271	0.1765	-0.0126	0.0569	-1.328	21.167	14.375
2	2.9553	-2.7866	1.074	16.012	-1.5606	2.278	0.1764	-0.0898	0.1103	-0.0513	-0.327	0.0508	0.0117	-0.1535	0.1506	0.1438	-0.0497	-0.0097	0.1839	-0.0401	0.0695	-0.39	26.279	13.674
3	15.6702	-4.5633	1.2735	7.791	1.9216	2.4537	-0.1203	0.4626	0.322	-0.357	-0.04	0.13	-0.07	0.1054	0.1604	0.1775	-0.0276	0.0053	0.1276	-0.0135	0.0364	2.094	30.045	4.321
4	11.0295	-7.3054	8.5392	36.6631	-13.1534	8.3949	0.2278	-0.0536	-0.5434	0.3211	-0.1461	-0.845	0.0412	0.0004	-0.0817	0.1596	-0.0153	-0.0288	0.1446	-0.0198	0.2495	9.983	18.613	8.561
5	81.5838	16.3958	7.5769	4.4509	-2.3567	13.8052	-0.1521	0.0857	-3.6858	-0.5774	-0.1827	-0.9721	2	0.6799	0.3348	0.7188	0.0475	-0.0072	0.1406	0.1022	0.7079	8.167	6.88	9.428
6	6.8417	6.3952	-8.6737	6.7212	-11.2222	29.1172	-0.2033	0.0892	-0.5618	-0.3997	-0.131	-0.4289	0.929	-0.2183	0.3343	0.186	0.0097	0.0613	0.3526	-0.1369	0.2066	5.226	14.344	0.228
7	7.705	1.5634	0.45	4.2498	-0.1006	2.9954	0.1041	0.0041	0.0748	-0.2686	-0.1259	0.1491	0.2506	-0.0342	0.0218	0.1772	-0.0091	-0.026	0.1073	-0.0214	0.0474	-6.08	21.6	2.37
8	7.5837	3.03	-3.4444	7.0897	0.6422	9.6456	0.0261	0.024	0.3622	-0.2669	-0.2117	0.6466	-0.3277	-0.6044	0.1857	0.0898	0.0241	-0.0528	0.1158	-0.0214	0.1467	-8.541	31.315	5.613
9	4.9628	0.8189	-2.4826	5.8788	4.2809	18.1033	0.233	0.1115	-0.0627	-0.0959	-0.2852	0.0572	0.1163	-0.5256	0.0522	0.1325	-0.017	-0.0228	0.1388	0.0209	0.0793	-5.333	21.093	9.196
10	3.1135	0.9777	0.7165	15.9329	-3.1208	2.1011	-0.0125	0.1322	0.0787	-0.2243	0.0019	-0.2701	0.0152	-0.0562	0.0105	0.1594	-0.0223	-0.0255	0.1652	-0.0179	0.0819	9.903	38.051	19.501
11	2.377	-2.3848	0.6281	12.8379	2.2013	1.6515	0.1087	-0.031	0.0069	-0.1309	-0.0688	-0.0769	-0.011	0.0221	-0.0399	0.151	-0.0252	-0.0012	0.1556	-0.0088	0.0703	9.353	32.51	17.774
12	6.9149	-3.4616	5.7008	8.1462	-4.4095	6.0414	-0.0535	0.4466	0.0188	-0.3091	0.0659	-0.4854	-0.0199	0.3817	-0.0124	0.1553	-0.0466	0.0262	0.1193	-0.0257	0.1065	12.801	31.442	8.327
13	13.9286	-18.8225	-5.5925	56.8049	8.3317	6.5919	-0.2527	0.1985	0.0931	-0.9651	0.0767	1.1206	-0.362	-0.3256	0.176	0.1739	-0.0227	-0.1272	0.1027	-0.015	0.1273	2.683	43.103	9.369
14	51.9474	-5.2244	25.1847	0.541	-2.383	14.4798	-1.0498	-0.286	1.0552	0.1013	0.0544	-0.04	-0.8936	0.1316	0.9954	0.3863	-0.0456	0.0529	0.1224	0.0186	0.3713	6.745	53.15	13.517
15	6.6176	-6.2167	-2.4548	28.5798	6.9353	12.2335	0.7187	0.3824	0.0538	-2.335	-0.4804	0.0817	-0.8889	0.0156	-0.2384	0.4298	-0.0584	0.0309	0.0842	-0.0201	0.1349	12.828	46.867	6.94
16	8.6218	-3.0235	2.285	11.3153	2.2895	8.8087	0.3881	0.669	0.5387	-0.9238	0.0377	-0.9054	-0.467	0.3321	-0.4258	0.1522	-0.0552	0.139	0.1231	-0.0296	0.2407	19.242	39.335	11.209
17	5.6151	2.8457	-2.6717	15.5246	3.0944	7.1577	0.0927	0.0139	0.191	-0.1902	0.6429	-2.1133	0.0253	0.6011	-0.7355	0.0121	0.0029	0.0366	0.1844	-0.1835	0.4356	23.47	32.246	13.401
18	3.0545	-0.288	0.3201	6.213	3.4962	7.4407	0.1217	0.0597	-0.0625	0.3482	0.1306	-0.5362	-0.0478	0.2176	-0.2523	0.0615	-0.0262	-0.0276	0.1234	-0.0419	0.1588	16.932	34.264	19.158

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	20 - 32
2	X-RAY DIFFRACTION	2	A	33 - 42
3	X-RAY DIFFRACTION	3	A	43 - 51
4	X-RAY DIFFRACTION	4	A	52 - 60
5	X-RAY DIFFRACTION	5	A	61 - 66
6	X-RAY DIFFRACTION	6	A	67 - 76
7	X-RAY DIFFRACTION	7	A	77 - 88
8	X-RAY DIFFRACTION	8	A	89 - 99
9	X-RAY DIFFRACTION	9	A	100 - 109
10	X-RAY DIFFRACTION	10	B	20 - 32
11	X-RAY DIFFRACTION	11	B	33 - 42
12	X-RAY DIFFRACTION	12	B	43 - 53
13	X-RAY DIFFRACTION	13	B	54 - 61
14	X-RAY DIFFRACTION	14	B	62 - 67
15	X-RAY DIFFRACTION	15	B	68 - 74
16	X-RAY DIFFRACTION	16	B	75 - 84
17	X-RAY DIFFRACTION	17	B	85 - 93
18	X-RAY DIFFRACTION	18	B	94 - 109

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