PDB-2qv8: Structure of the minor pseudopilin EpsH from the Type 2 Secretion...

ID or keywords:

Entry

Database: PDB / ID: 2qv8

Title

Structure of the minor pseudopilin EpsH from the Type 2 Secretion System of Vibrio cholerae

Components

General secretion pathway protein H

Keywords

TRANSPORT PROTEIN / minor pseudopilin /

Methylation / Transport

Function / homology

Function and homology information

protein secretion by the type II secretion system /

type II protein secretion system complex /

plasma membrane
Similarity search - Function

Biological species

Vibrio cholerae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2 Å

Authors

Yanez, M.E. / Korotkov, K.V. / Abendroth, J. / Hol, W.G.J.

Citation

Journal: J.Mol.Biol. / Year: 2008
Title: Structure of the minor pseudopilin EpsH from the Type 2 secretion system of Vibrio cholerae.
Authors: Yanez, M.E. / Korotkov, K.V. / Abendroth, J. / Hol, W.G.

History

Deposition	Aug 7, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 26, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2qv8.cif.gz	72.9 KB	Display	PDBx/mmCIF format
PDB format	pdb2qv8.ent.gz	59.3 KB	Display	PDB format
PDBx/mmJSON format	2qv8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qv/2qv8 ftp://data.pdbj.org/pub/pdb/validation_reports/qv/2qv8	HTTPS FTP

-
Related structure data

Similar structure data	2hb5-d 6r58-3 4r9w-d 4b6c-1 2bzu-d 4b6c-2 1iwq-d 6h5z-d 6r5c-2 4hjz-2 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

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#211 - Jul 2017 Pilus Machine similarity (2)

Deposited unit

A: General secretion pathway protein H

B: General secretion pathway protein H

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

1

A: General secretion pathway protein H

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

2

B: General secretion pathway protein H

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

Unit cell

Length a, b, c (Å)	53.349, 70.449, 85.100
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	A
4	1	B

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-ID	Component-ID	Beg label comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ASP	LYS	A	A	30 - 159	1 - 130
2	1	ASP	LYS	B	B	30 - 159	1 - 130
3	2	TRP	GLU	A	A	167 - 184	138 - 155
4	2	TRP	GLU	B	B	167 - 184	138 - 155

Details

The biological unit is a monomer. There are 2 biological units in the asymmetric unit (chains A & B).

#1: Protein	General secretion pathway protein H / Cholera toxin secretion protein epsH Mass: 18205.965 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: epsH / Plasmid: pET21d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P45774
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

General secretion pathway protein H / Cholera toxin secretion protein epsH

Mass: 18205.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Vibrio cholerae (bacteria) / Gene: epsH / Plasmid: pET21d / Species (production host): Escherichia coli / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P45774

#2: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.2 Å³/Da / Density % sol: 43.99 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion / pH: 4.5 Details: PEG 4000, pH 4.5, vapor diffusion, temperature 298K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL9-2 / Wavelength: 0.97903 Å

Detector

Type: MARRESEARCH / Detector: CCD / Date: Jul 16, 2005

Radiation

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

Radiation wavelength

Wavelength: 0.97903 Å / Relative weight: 1

Reflection

Redundancy: 7.1 % / Av σ(I) over netI: 11.5 / Number: 149297 / R_merge(I) obs: 0.07 / Χ²: 1.08 / D res high: 1.99 Å / D res low: 50 Å / Num. obs: 21140 / % possible obs: 93.2

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
4.29	50	99.9	1	0.043	1.046	6.8
3.4	4.29	78.2	1	0.049	1.154	6.5
2.97	3.4	100	1	0.056	1.02	7.3
2.7	2.97	100	1	0.074	1.102	7.3
2.51	2.7	100	1	0.094	1.054	7.3
2.36	2.51	100	1	0.116	1.069	7.3
2.24	2.36	76.3	1	0.159	1.109	6.8
2.14	2.24	77.1	1	0.201	1.17	6.9
2.06	2.14	100	1	0.221	1.073	7.3
1.99	2.06	100	1	0.271	1.068	6.9

Reflection

Resolution: 1.99→50 Å / Num. obs: 21140 / % possible obs: 93.2 % / Redundancy: 7.1 % / R_merge(I) obs: 0.07 / Χ²: 1.081 / Net I/σ(I): 11.5

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
1.99-2.06	6.9	0.271	2231	1.068	1	100
2.06-2.14	7.3	0.221	2218	1.073	1	100
2.14-2.24	6.9	0.201	1714	1.17	1	77.1
2.24-2.36	6.8	0.159	1714	1.109	1	76.3
2.36-2.51	7.3	0.116	2246	1.069	1	100
2.51-2.7	7.3	0.094	2253	1.054	1	100
2.7-2.97	7.3	0.074	2256	1.102	1	100
2.97-3.4	7.3	0.056	2272	1.02	1	100
3.4-4.29	6.5	0.049	1794	1.154	1	78.2
4.29-50	6.8	0.043	2442	1.046	1	99.9

-
Phasing

Phasing	Method: SAD

-
Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SOLVE		phasing
REFMAC		refinement
PDB_EXTRACT	3	data extraction
HKL-2000		data collection

Refinement

Method to determine structure:

SAD / Resolution: 2→20 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.929 / SU B: 6.33 / SU ML: 0.094 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.184 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.212	1072	5.2 %	RANDOM
R_work	0.169	-	-	-
obs	0.171	20721	93.01 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 12.33 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.62 Å²	0 Å²	0 Å²
2-	-	-1.12 Å²	0 Å²
3-	-	-	0.5 Å²

Refinement step

Cycle: LAST / Resolution: 2→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2117	0	0	301	2418

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.022	2282
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1545
X-RAY DIFFRACTION	r_angle_refined_deg	1.537	1.968	3123
X-RAY DIFFRACTION	r_angle_other_deg	0.94	3	3795
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.547	5	299
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.845	25.391	115
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.008	15	396
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.241	15	14
X-RAY DIFFRACTION	r_chiral_restr	0.094	0.2	350
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	2605
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	454
X-RAY DIFFRACTION	r_nbd_refined	0.204	0.2	423
X-RAY DIFFRACTION	r_nbd_other	0.2	0.2	1534
X-RAY DIFFRACTION	r_nbtor_refined	0.176	0.2	1072
X-RAY DIFFRACTION	r_nbtor_other	0.085	0.2	1242
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.261	0.2	226
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.043	0.2	1
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.167	0.2	23
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.237	0.2	60
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.398	0.2	55
X-RAY DIFFRACTION	r_mcbond_it	1.053	1.5	1541
X-RAY DIFFRACTION	r_mcbond_other	0.348	1.5	565
X-RAY DIFFRACTION	r_mcangle_it	1.384	2	2270
X-RAY DIFFRACTION	r_scbond_it	2.47	3	965
X-RAY DIFFRACTION	r_scangle_it	3.608	4.5	842

Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Number	Type	Rms dev position (Å)	Weight position
638	MEDIUM POSITIONAL	0.27	0.5
793	LOOSE POSITIONAL	0.6	5
638	MEDIUM THERMAL	2.55	2
793	LOOSE THERMAL	3.07	10

LS refinement shell

Resolution: 2→2.051 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.232	80	-
R_work	0.171	1534	-
all	-	1614	-
obs	-	-	99.94 %

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	5.088	-2.7775	1.4093	7.4885	-1.4931	3.1544	0.015	-0.0408	-0.2923	0.1089	-0.0144	0.1749	0.2186	-0.011	-0.0007	0.0341	-0.0191	-0.0014	0.0445	-0.0148	0.0497	28.5329	16.5468	33.405
2	3.3845	-1.7563	3.3101	2.875	-2.4615	5.1058	-0.1775	-0.0227	0.1462	0.0789	0.0111	-0.0074	-0.1946	-0.053	0.1664	0.0488	-0.001	0.0111	0.0287	-0.0087	0.0627	30.4854	29.073	32.5012
3	2.171	0.1416	0.059	13.5476	-5.5445	2.9063	-0.0098	-0.0943	0.1768	0.4767	0.0233	0.3112	-0.2558	-0.0621	-0.0135	0.0699	0.0154	0.0218	0.0395	-0.0313	0.0597	30.3865	35.4592	36.842
4	11.1294	4.1842	-0.4191	3.1866	-2.0773	2.2997	0.0124	0.0592	0.3309	0.3436	0.0857	0.2536	-0.1417	-0.1487	-0.0981	0.032	0.0366	0.0326	0.0485	0.0166	0.0266	21.9991	30.577	37.3254
5	3.1904	-1.7252	0.3475	3.1896	-0.6803	0.8282	-0.1669	-0.2475	-0.2344	0.2508	0.129	0.1503	-0.0155	-0.0016	0.0379	0.0775	-0.0207	-0.0095	0.0592	-0.0088	0.0586	37.0562	19.1238	41.1764
6	0.9612	-0.6269	2.539	1.384	-1.5368	12.2237	-0.0317	0.0689	0.0202	0.0478	0.0524	0.0287	-0.3773	-0.0958	-0.0207	0.016	-0.0063	0.0029	0.0222	0.0223	0.0931	47.8963	21.6106	43.4059
7	1.7719	-0.5233	0.0634	2.2556	-0.6683	0.922	-0.0294	-0.0482	0.0369	0.0838	0.031	-0.0354	-0.0499	0.0101	-0.0016	0.0607	-0.0091	-0.007	0.0595	-0.0078	0.0453	38.7101	21.381	34.385
8	3.913	-3.8755	1.9376	11.5635	-2.8986	1.0837	-0.1267	0.7271	0.2045	-1.0509	-0.1075	-0.7154	0.1505	0.2082	0.2342	0.0745	-0.0623	0.0096	0.0556	-0.009	-0.0217	37.5513	15.1985	23.7529
9	6.7777	-7.6557	0.298	17.517	-3.0341	3.5514	0.0401	-0.0533	-0.0035	0.3468	0.0895	0.5719	-0.2911	-0.2982	-0.1296	0.0188	0.0168	0.0071	0.0144	0.0179	0.0745	12.245	30.2432	17.7378
10	3.5307	-0.8983	1.646	4.0162	0.4978	3.6735	0.0506	0.049	0.1205	-0.0911	-0.0198	0.1942	0.0807	-0.3012	-0.0308	0.0528	-0.0083	0.0004	0.0636	0.0172	0.0673	16.1511	15.8857	18.1665
11	3.2467	-2.1048	0.4653	5.7682	2.7275	2.1504	-0.0996	-0.2576	-0.0219	0.5571	-0.1465	0.5072	0.0917	-0.1344	0.2461	0.0667	-0.0191	0.0428	0.0165	-0.0231	0.0589	11.4124	8.4218	19.9804
12	2.0651	2.1391	-0.9095	8.5846	-7.1024	6.3591	-0.2097	0.1244	0.1654	0.035	0.2847	0.8147	-0.0042	-0.3796	-0.075	0.0511	0.0428	-0.0489	0.0697	-0.0479	0.1462	7.2572	23.3506	13.4335
13	5.8781	-2.1838	2.8653	3.5532	0.733	5.0364	0.2076	0.4037	0.0418	-0.2378	-0.1773	-0.0905	-0.1752	0.1209	-0.0303	0.1253	0.0227	-0.0121	0.0591	-0.0023	0.0447	18.8295	12.0364	11.0573
14	0.993	-1.1557	-0.6877	8.5918	0.9209	0.4782	0.1804	0.1688	0.2333	-0.8808	-0.1011	0.2175	0.032	-0.1406	-0.0792	0.1223	0.0257	-0.0569	0.0232	0.024	0.0486	14.2448	30.0465	8.0823
15	11.6143	-11.2689	3.2978	21.1044	-0.4027	7.4901	0.3921	0.6049	0.6098	-0.6514	-0.4125	-1.8409	-0.1963	0.8277	0.0204	0.0478	-0.0226	0.0637	0.0194	0.0426	0.178	25.518	24.0163	11.6498
16	13.6778	-13.725	1.3796	38.2818	-10.9486	3.8714	0.6044	0.3002	1.2749	-0.8591	-0.7413	-2.081	-0.0148	0.5057	0.1369	0.0139	-0.0012	0.0326	-0.0113	0.0547	0.1935	21.8714	34.0896	12.3765

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	30 - 45	1 - 16
2	X-RAY DIFFRACTION	2	A	A	46 - 66	17 - 37
3	X-RAY DIFFRACTION	3	A	A	67 - 79	38 - 50
4	X-RAY DIFFRACTION	4	A	A	80 - 88	51 - 59
5	X-RAY DIFFRACTION	5	A	A	89 - 103	60 - 74
6	X-RAY DIFFRACTION	6	A	A	104 - 119	75 - 90
7	X-RAY DIFFRACTION	7	A	A	120 - 171	91 - 142
8	X-RAY DIFFRACTION	8	A	A	172 - 186	143 - 157
9	X-RAY DIFFRACTION	9	B	B	30 - 39	1 - 10
10	X-RAY DIFFRACTION	10	B	B	40 - 67	11 - 38
11	X-RAY DIFFRACTION	11	B	B	68 - 86	39 - 57
12	X-RAY DIFFRACTION	12	B	B	87 - 101	58 - 72
13	X-RAY DIFFRACTION	13	B	B	102 - 148	73 - 119
14	X-RAY DIFFRACTION	14	B	B	149 - 167	120 - 138
15	X-RAY DIFFRACTION	15	B	B	168 - 178	139 - 149
16	X-RAY DIFFRACTION	16	B	B	179 - 184	150 - 155

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Phasing

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi