PDB-4pho: ClyA CC6/264 ox (2-303)

ID or keywords:

Entry

Database: PDB / ID: 4pho

Title

ClyA CC6/264 ox (2-303)

Components

Hemolysin E, chromosomal

Keywords

TOXIN / alpha pore-forming toxin / intramolecular disulfide bond

Function / homology

Function and homology information

modulation of apoptotic process in another organism /

hemolysis in another organism /

toxin activity /

periplasmic space / host cell plasma membrane / extracellular region /

membrane / identical protein binding
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.123 Å

Authors

Roderer, D.J.A. / Glockshuber, R. / Ban, N.

Citation

Journal: Biochemistry / Year: 2014
Title: Characterization of Variants of the Pore-Forming Toxin ClyA from Escherichia coli Controlled by a Redox Switch.
Authors: Roderer, D. / Benke, S. / Muller, M. / Fah-Rechsteiner, H. / Ban, N. / Schuler, B. / Glockshuber, R.

History

Deposition	May 6, 2014	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Sep 24, 2014	Provider: repository / Type: Initial release
Revision 1.1	Oct 1, 2014	Group: Database references
Revision 1.2	Oct 29, 2014	Group: Database references
Revision 1.3	Dec 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4pho.cif.gz	366.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4pho.ent.gz	301.4 KB	Display	PDB format
PDBx/mmJSON format	4pho.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ph/4pho ftp://data.pdbj.org/pub/pdb/validation_reports/ph/4pho	HTTPS FTP

-
Related structure data

Related structure data	4phqC 1qoyS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4phq-4 1hvv-d 4phq-1 5le9-d 4kzd-3 3dyj-1 1qoy-d 4i3m-1 3597 5u6f-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) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

4phqC

1qoyS

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Hemolysin E, chromosomal

B: Hemolysin E, chromosomal

C: Hemolysin E, chromosomal

hetero molecules

101 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Hemolysin E, chromosomal

hetero molecules

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

2

B: Hemolysin E, chromosomal

hetero molecules

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

3

C: Hemolysin E, chromosomal

hetero molecules

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

Unit cell

Length a, b, c (Å)	94.920, 125.600, 186.810
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	C-501- HOH

Details

biological unit is a monomer

#1: Protein	Hemolysin E, chromosomal / Cytotoxin ClyA / Hemolysis-inducing protein / Latent pore-forming 34 kDa hemolysin / Silent hemolysin SheA Mass: 33636.168 Da / Num. of mol.: 3 / Mutation: A6C, V264C, C87A, C285A Source method: isolated from a genetically manipulated source Details: 4 Quick-change PCRs to introduce point mutations, TEV cleavage of N-terminal His(6)-tag Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: hlyE, clyA, hpr, sheA, ycgD, b1182, JW5181 / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Tuner / References: UniProt: P77335
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 363 / 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: 2.76 Å³/Da / Density % sol: 55.42 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 21% PEG 3350, 0.1 M Tris-Acetate / PH range: 6.2-7.0

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SLS

/ Beamline: X06SA / Wavelength: 1 Å

Detector

Type: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 7, 2012

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.12→50 Å / Num. obs: 63155 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 3.33 % / B_iso Wilson estimate: 39.62 Å² / R_merge F obs: 1 / R_merge(I) obs: 0.064 / R_rim(I) all: 0.067 / Χ²: 0.987 / Net I/σ(I): 21.63 / Num. measured all: 710409

Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)	Highest resolution (Å)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
2.12-2.25		0.924	0.861	3.1	108790	10285	9986	0.903	97.1
2.25-2.41		0.97	0.542	4.91	112115	9756	9754	0.567	100
2.41-2.6		0.987	0.332	7.66	100426	8720	8717	0.347	100
2.6-2.84		0.995	0.188	12.05	87360	7975	7975	0.197	100
2.84-3.18		0.998	0.107	20.96	89139	7594	7594	0.112	100
3.18-3.67		0.999	0.06	33.98	72656	6580	6580	0.063	100
3.67-4.49		1	0.037	53.48	65155	5606	5606	0.039	100
4.49-6.32		1	0.032	58.69	47887	4385	4385	0.033	100
	6.32	1	0.025	72.16	26881	2565	2558	0.026	99.7

-
Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	2.5 Å	48.08 Å
Translation	2.5 Å	48.08 Å

-
Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE	2.3.0	data scaling
PDB_EXTRACT	3.14	data extraction
PHASER		phasing
PHENIX	(phenix.refine: 1.8.1_1168)	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1QOY

1qoy

Resolution: 2.123→48.097 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.32 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2308	3020	5.11 %
R_work	0.1851	56131	-
obs	0.1875	59151	93.5 %

Solvent computation

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

Displacement parameters

B_iso max: 182.21 Å² / B_iso mean: 72.8436 Å² / B_iso min: 31.69 Å²

Refinement step

Cycle: final / Resolution: 2.123→48.097 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6838	0	32	363	7233
B_iso mean	-	-	79.17	64.34	-
Num. residues	-	-	-	-	872

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	6997
X-RAY DIFFRACTION	f_angle_d	0.888	9435
X-RAY DIFFRACTION	f_chiral_restr	0.061	1100
X-RAY DIFFRACTION	f_plane_restr	0.003	1191
X-RAY DIFFRACTION	f_dihedral_angle_d	14.878	2599

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 (%)
2.1225-2.1557	0.3533	124	0.2929	2072	X-RAY DIFFRACTION	78
2.1557-2.1911	0.3363	126	0.277	2239	X-RAY DIFFRACTION	82
2.1911-2.2288	0.354	127	0.245	2246	X-RAY DIFFRACTION	84
2.2288-2.2694	0.3074	130	0.2454	2252	X-RAY DIFFRACTION	84
2.2694-2.313	0.2779	129	0.2237	2369	X-RAY DIFFRACTION	87
2.313-2.3602	0.281	121	0.2143	2380	X-RAY DIFFRACTION	88
2.3602-2.4115	0.2711	120	0.2	2417	X-RAY DIFFRACTION	89
2.4115-2.4676	0.2552	136	0.197	2496	X-RAY DIFFRACTION	91
2.4676-2.5293	0.227	135	0.1842	2512	X-RAY DIFFRACTION	93
2.5293-2.5977	0.2427	135	0.1835	2564	X-RAY DIFFRACTION	95
2.5977-2.6742	0.2458	137	0.1911	2585	X-RAY DIFFRACTION	96
2.6742-2.7605	0.2846	135	0.1996	2614	X-RAY DIFFRACTION	96
2.7605-2.8591	0.2648	141	0.2	2658	X-RAY DIFFRACTION	97
2.8591-2.9736	0.2491	144	0.1985	2654	X-RAY DIFFRACTION	98
2.9736-3.1089	0.2588	143	0.2013	2685	X-RAY DIFFRACTION	99
3.1089-3.2728	0.2535	147	0.2062	2759	X-RAY DIFFRACTION	99
3.2728-3.4778	0.2593	143	0.1866	2696	X-RAY DIFFRACTION	100
3.4778-3.7462	0.2265	148	0.1718	2756	X-RAY DIFFRACTION	100
3.7462-4.123	0.1773	147	0.1513	2737	X-RAY DIFFRACTION	100
4.123-4.7192	0.2003	147	0.1444	2754	X-RAY DIFFRACTION	100
4.7192-5.9439	0.2114	149	0.1818	2801	X-RAY DIFFRACTION	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	2.2193	-0.166	-1.943	1.1969	1.1341	4.7834	-0.1814	-0.1178	-0.2014	0.1691	0.2002	0.0212	0.2805	1.0983	-0.0088	0.287	0.1276	-0.0025	0.7027	0.0381	0.3175	-21.8732	-28.4429	32.382
2	2.7441	0.2009	-1.0629	1.24	0.7573	4.8165	-0.0278	0.6099	-0.1235	-0.4833	0.3624	-0.0331	-1.0514	0.8869	-0.2407	0.4015	-0.034	0.0038	0.9821	-0.017	0.4181	-16.4847	-26.4385	8.1197
3	4.54	-0.9013	-1.1249	4.7396	1.8469	3.854	-0.0591	-0.2043	0.0455	0.4497	-0.2828	0.3183	-0.0062	0.3918	0.3023	0.3469	0.0258	0.0649	0.4544	0.0984	0.2772	-34.6936	-19.6524	49.3913
4	1.918	-0.2445	0.0195	0.9263	0.1316	7.9878	-0.1496	0.4366	-0.396	0.1451	0.0236	0.1287	1.1165	0.286	0.0823	0.4733	0.0968	0.0759	0.5389	-0.1227	0.4768	-31.87	-44.2316	9.4485
5	1.6701	-0.0329	-0.2861	1.6398	-2.0048	3.5183	-0.1779	-0.3377	-0.4032	0.5804	0.0141	0.2947	1.798	-0.1615	0.1825	0.7177	0.0464	0.1923	0.4577	0.002	0.6403	-35.5567	-47.4225	29.6353
6	1.5062	-0.1084	1.8011	1.2472	-0.5132	2.3233	-0.2518	1.019	-0.0008	-0.1146	-0.0424	0.267	-0.0078	-0.2213	0.2388	0.3361	0.0516	-0.0239	1.298	-0.1521	0.4491	-41.4967	-35.7814	-11.346
7	3.9578	4.5215	-5.733	5.154	-6.549	8.3066	0.6318	1.5684	-0.2252	-2.7401	0.2581	1.09	-0.7619	-0.3316	-0.8294	1.3201	0.0765	-0.239	1.6062	0.1341	0.6084	-29.6121	-21.2237	-0.9458
8	1.9209	-0.0447	-0.1006	1.5133	0.8846	4.3115	0.2429	0.1853	0.3879	-0.1303	-0.1467	-0.0965	-0.8404	0.8111	-0.1181	0.5619	-0.1089	0.0941	0.4576	0.1188	0.443	-35.8199	-1.4486	37.3953
9	2.4222	0.2759	0.9607	1.6356	1.1956	5.1874	0.4356	-1.0479	0.5456	0.4409	-0.0606	-0.0073	-0.3451	0.9365	-0.2946	0.5873	-0.2373	0.0397	0.6781	-0.0766	0.4645	-36.508	-0.683	62.0209
10	1.5975	-0.6446	-1.9898	3.6852	2.3544	3.2547	-0.1642	0.8098	-0.1492	0.1154	-0.1629	0.2809	0.912	0.0079	0.4237	0.5663	0.1514	0.0873	0.8841	0.1265	0.3938	-35.2189	-15.4512	19.1128

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 5:164)	A	5 - 164
2	X-RAY DIFFRACTION	2	(chain A and resid 165:260)	A	165 - 260
3	X-RAY DIFFRACTION	3	(chain A and resid 261:295)	A	261 - 295
4	X-RAY DIFFRACTION	4	(chain B and resid 6:166)	B	6 - 166
5	X-RAY DIFFRACTION	5	(chain B and resid 167:260)	B	167 - 260
6	X-RAY DIFFRACTION	6	(chain B and resid 261:293)	B	261 - 293
7	X-RAY DIFFRACTION	7	(chain B and resid 294:299)	B	294 - 299
8	X-RAY DIFFRACTION	8	(chain C and resid 6:164)	C	6 - 164
9	X-RAY DIFFRACTION	9	(chain C and resid 165:260)	C	165 - 260
10	X-RAY DIFFRACTION	10	(chain C and resid 261:299)	C	261 - 299

-
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