PDB-5kko: A 1.55A X-Ray Structure from Vibrio cholerae O1 biovar El Tor of ...

ID or keywords:

Entry

Database: PDB / ID: 5kko

Title

A 1.55A X-Ray Structure from Vibrio cholerae O1 biovar El Tor of a Hypothetical Protein

Components

Uncharacterised protein

Keywords

STRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha helical protein / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Uncharacterized protein / Uncharacterized protein

Function and homology information

Biological species

Vibrio cholerae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.55 Å

Authors

Brunzelle, J.S. / Wawrzak, Z. / Skarina, T. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To Be Published
Title: A 1.55A X-Ray Structure from Vibrio cholerae O1 biovar El Tor of a Hypothetical Protein
Authors: Brunzelle, J.S. / Wawrzak, Z. / Skarina, T. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Jun 22, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 21, 2016	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5kko.cif.gz	148.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5kko.ent.gz	127.2 KB	Display	PDB format
PDBx/mmJSON format	5kko.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5kko_validation.pdf.gz	472.7 KB	Display	wwPDB validaton report
Full document	5kko_full_validation.pdf.gz	479.2 KB	Display
Data in XML	5kko_validation.xml.gz	16.2 KB	Display
Data in CIF	5kko_validation.cif.gz	23.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kk/5kko ftp://data.pdbj.org/pub/pdb/validation_reports/kk/5kko	HTTPS FTP

-
Related structure data

Similar structure data	4a6h-d 2fyi-2 2fyi-3 4l69-1 6yva-d 1gri-d 4ofx-1 3khh-1 1zql-d 3tw8-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: CSGID-IDP95006

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Uncharacterised protein

B: Uncharacterised protein

C: Uncharacterised protein

D: Uncharacterised protein

E: Uncharacterised protein

F: Uncharacterised protein

39.3 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Uncharacterised protein

D: Uncharacterised protein

E: Uncharacterised protein

B: Uncharacterised protein

C: Uncharacterised protein

F: Uncharacterised protein

defined by author&software
39.3 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	56.870, 68.240, 69.460
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Uncharacterised protein Mass: 6548.084 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: ERS013202_03616 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: A0A0H7H6M3, UniProt: A0A655ZDK1*PLUS
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Uncharacterised protein

Mass: 6548.084 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Vibrio cholerae (bacteria) / Gene: ERS013202_03616 / Plasmid: pMCSG53 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: A0A0H7H6M3, UniProt: A0A655ZDK1*PLUS

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal grow	Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 3.5 / Details: 20% PEG3350, 0.1M Citr. Ac. pH 3.5, MgSulph 0.2M

-
Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	APS	21-ID-D	1	1.1272
SYNCHROTRON	APS	21-ID-D	2	0.97856

Detector

Type	ID	Detector	Date	Details
MARMOSAIC 300 mm CCD	1	CCD	Nov 9, 2014	Mirrors
MARMOSAIC 300 mm CCD	2	CCD	Nov 7, 2014	Mirrors

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	Si 111	SINGLE WAVELENGTH	M	x-ray	1
2	Si 111	SINGLE WAVELENGTH	M	x-ray	2

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1.1272	1
2	0.97856	1

Reflection

Resolution: 1.55→22 Å / Num. obs: 39875 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / CC_1/2: 0.997 / R_merge(I) obs: 0.089 / Net I/σ(I): 11.5

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Diffraction-ID	% possible all
1.55-1.59	5.4	0.757	2.5	1	99.9
1.58-1.62	8.6	0.639	3.2	2	100

-
Processing

Software

Name	Version	Classification
Aimless	0.3.11	data scaling
PHENIX	dev_2203	refinement
PDB_EXTRACT	3.2	data extraction
xia2	0.3.7.0	data reduction
PHENIX	dev_1839	phasing
PHASER	2.6.1	phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.55→22 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.51

	R_factor	Num. reflection	% reflection
R_free	0.2057	1959	4.92 %
R_work	0.1713	-	-
obs	0.173	39821	99.8 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 128.2 Å² / B_iso mean: 28.4863 Å² / B_iso min: 7.26 Å²

Refinement step

Cycle: final / Resolution: 1.55→22 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2578	0	0	227	2805
B_iso mean	-	-	-	32.89	-
Num. residues	-	-	-	-	313

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.017	2766
X-RAY DIFFRACTION	f_angle_d	1.525	3776
X-RAY DIFFRACTION	f_chiral_restr	0.104	443
X-RAY DIFFRACTION	f_plane_restr	0.01	492
X-RAY DIFFRACTION	f_dihedral_angle_d	17.636	1742

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.55-1.5888	0.2977	113	0.2342	2697	2810	100
1.5888-1.6317	0.2587	138	0.2226	2653	2791	100
1.6317-1.6797	0.223	146	0.2083	2675	2821	100
1.6797-1.7339	0.2359	135	0.1977	2678	2813	100
1.7339-1.7959	0.2247	161	0.1871	2642	2803	100
1.7959-1.8677	0.2377	129	0.1823	2679	2808	100
1.8677-1.9527	0.2104	115	0.1805	2724	2839	100
1.9527-2.0556	0.2148	138	0.1764	2680	2818	100
2.0556-2.1843	0.2079	159	0.1602	2691	2850	100
2.1843-2.3527	0.1975	168	0.1606	2679	2847	100
2.3527-2.5892	0.2106	149	0.1691	2695	2844	100
2.5892-2.963	0.2236	134	0.1718	2733	2867	100
2.963-3.7302	0.1746	122	0.1523	2768	2890	99
3.7302-22.0036	0.1848	152	0.1623	2868	3020	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	6.9347	-4.5202	-5.2899	5.7761	5.1522	6.4464	0.0788	0.4236	-0.0757	-0.0144	0.0333	-0.2982	0.1434	-0.3118	-0.1454	0.4006	0.0029	-0.0429	0.1688	-0.0199	0.271	48.9118	4.4752	43.9478
2	3.3223	1.8546	0.0231	5.7859	0.6787	3.7531	0.1317	0.0335	0.0664	0.0388	-0.1237	0.3322	-0.0717	-0.3672	-0.0519	0.0684	0.0029	-0.0059	0.1215	-0.0046	0.0555	40.5816	21.7433	49.9864
3	3.0271	-2.5518	1.1219	4.9428	-0.733	2.7325	0.1631	0.0259	0.1191	-0.1173	-0.1227	-0.4013	0.0001	0.2397	-0.0547	0.0753	-0.001	0.0251	0.0989	-0.009	0.0819	50.7202	21.3602	50.102
4	7.1292	-2.9637	-2.9399	5.336	5.0592	7.4135	0.0813	-0.1584	0.12	-0.0867	-0.1895	0.0958	-0.1348	0.0746	0.0428	0.1719	-0.011	-0.0339	0.1918	0.0298	0.1601	52.0804	16.7974	60.5007
5	1.6676	1.6459	1.3951	5.2839	3.4329	3.3011	-0.1332	0.1031	0.1791	0.0322	0.144	-0.1744	-0.4148	-0.0163	-0.0028	0.1735	0.0188	-0.0063	0.151	0.0094	0.1651	45.8884	57.2121	35.1923
6	3.2003	2.0077	1.5622	2.9272	1.3917	3.3844	-0.0397	0.0531	0.0389	-0.1522	-0.018	0.0156	0.0424	0.1397	0.0578	0.0512	0.0094	0.0095	0.0841	-0.0032	0.0846	51.3591	45.5359	31.9243
7	3.4448	-0.1809	-1.5953	0.8876	-2.0735	6.4853	0.3061	0.8014	1.1345	-0.3328	0.1292	-1.319	-1.482	0.3281	-0.1804	0.4098	-0.034	0.1062	0.41	0.1318	0.6267	56.8525	55.2273	25.2256
8	3.2057	-2.2152	2.809	3.142	-4.0357	5.2079	-0.2881	0.1438	0.478	-0.7565	-0.0408	-0.0975	-0.3456	0.1995	0.3711	0.404	0.0655	-0.0495	0.2138	0.0608	0.2682	42.0843	64.0384	31.6878
9	3.0362	1.5833	-0.133	5.661	-0.9124	3.5635	0.0719	-0.08	0.1366	0.2355	-0.0718	-0.1547	-0.0452	-0.0795	-0.025	0.082	-0.0231	-0.0128	0.0962	0.0049	0.1017	52.7077	48.9279	43.449
10	5.1348	-5.1472	1.8933	6.0102	-2.3014	1.6611	0.0309	0.0937	0.068	0.0511	-0.045	-0.018	0.0157	-0.1908	-0.0619	0.0739	0.0105	0.0217	0.1209	-0.0017	0.0931	43.8182	46.7947	40.3492
11	2.4608	-1.8292	-2.5214	1.4037	2.0443	3.3593	0.3337	-0.6564	0.5686	0.0314	-0.0213	-0.2282	-0.1468	0.4169	-0.1988	0.1656	-0.029	0.012	0.2318	-0.0064	0.2079	23.5609	57.8442	45.3757
12	4.313	-1.3026	2.119	2.6778	-1.2593	1.2089	0.1047	-0.9148	-0.2896	0.6246	0.2552	0.1838	0.5318	-0.2865	0.2975	0.5148	-0.0267	-0.0077	0.2203	0.0206	0.1562	41.0497	5.1871	47.8119
13	6.4751	3.4667	1.3512	2.6041	0.4516	2.0769	-0.1346	0.1681	-0.0654	-0.5347	0.1672	-0.0751	0.492	0.2844	-0.0351	0.2138	0.0522	0.0356	0.1397	0.0107	0.1239	53.6139	15.089	40.7771
14	3.6099	-3.0265	-3.0736	6.5883	-2.4298	8.8057	0.2873	-0.2348	0.7528	-0.1515	-0.1581	-1.1095	-0.2729	0.7475	0.0035	0.1375	-0.0291	0.0452	0.1277	-0.0251	0.2075	55.1563	28.7068	38.2891
15	6.0558	4.61	-0.5997	4.2842	-0.1671	2.704	0.0147	0.011	-0.1997	-0.1569	0.04	-0.1537	0.1529	-0.1038	-0.067	0.1445	-0.0043	-0.0197	0.1029	-0.0001	0.0891	44.4535	21.2778	40.1878
16	8.6573	1.3075	1.2502	6.2411	-0.4757	6.1529	0.2031	0.2684	0.3765	-0.2885	-1.1472	-1.3565	-0.6278	1.0552	0.7615	0.5688	-0.1319	-0.0398	0.6464	0.1373	0.5837	29.5608	9.5927	39.0065
17	5.9831	0.7004	2.4142	1.4785	-0.097	1.0697	0.3328	-0.5293	0.4117	0.6907	0.5501	0.0196	-0.1344	0.1615	1.6006	0.563	-0.0211	0.0933	0.3383	-0.1321	0.2358	43.483	65.5487	60.5151
18	6.9556	1.0104	0.0044	7.286	-0.8454	5.6126	-0.1441	0.0133	0.2967	0.0234	0.0731	-0.0767	-0.4077	-0.034	0.0897	0.1375	0.0195	0.0154	0.1154	0.0199	0.1075	38.9444	53.1914	49.8124
19	6.9875	-5.2791	6.8175	4.1185	-4.9441	7.0195	0.2414	-0.3415	-0.4308	-0.1707	0.1654	0.5326	0.5584	-0.7546	-0.2288	0.1464	-0.0011	0.0141	0.1398	0.0073	0.1501	40.6727	39.1167	48.5836
20	3.723	3.1265	1.8273	4.1818	3.3317	4.6293	0.0079	-0.3036	0.2878	0.168	-0.0895	0.297	-0.0886	0.2303	0.0259	0.1022	-0.0152	0.0242	0.1462	-0.0293	0.1062	46.6908	48.6501	55.4213
21	3.2432	5.3275	-3.4605	9.3082	-4.4438	5.707	-0.8188	1.5239	-0.6777	-1.2218	1.0711	-0.3475	-0.0778	-0.9712	-0.7503	0.6932	-0.2012	0.0413	0.7311	0.021	1.0688	57.9295	73.7366	52.9502
22	5.8872	-0.0856	1.4202	4.4581	4.1548	4.2841	-0.0737	0.4153	-0.2898	-0.6645	0.6186	-0.2898	1.3251	0.1696	0.1001	0.7382	-0.0037	-0.0045	0.2247	-0.0779	0.2626	46.7535	1.1514	16.3921
23	7.4837	-3.3384	-0.9738	6.8489	1.5956	6.4943	-0.23	-0.2268	0.0781	0.0378	0.3152	-0.2832	0.3973	0.0179	-0.0995	0.2368	-0.0209	-0.0269	0.2036	-0.0084	0.1355	41.7554	14.885	30.0277
24	6.267	5.6389	-6.1486	6.3838	-6.0951	6.3044	0.0146	0.3098	0.3296	-0.1845	0.2878	0.7799	0.171	-0.4545	-0.2423	0.2148	0.0204	-0.0203	0.1067	0.0074	0.1371	43.7538	28.7705	32.2118
25	4.0856	-1.8126	-2.1973	3.8106	3.8831	5.6059	0.0223	0.1467	-0.3167	0.1033	-0.1616	0.0189	0.1717	0.0488	-0.0179	0.1454	0.0327	-0.0454	0.1265	-0.016	0.1054	50.3819	18.881	24.2148

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 1 through 7 )	A	1 - 7
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 8 through 24 )	A	8 - 24
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 25 through 40 )	A	25 - 40
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 41 through 52 )	A	41 - 52
5	X-RAY DIFFRACTION	5	chain 'B' and (resid -2 through 19 )	B	-2 - 19
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 20 through 40 )	B	20 - 40
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 41 through 50 )	B	41 - 50
8	X-RAY DIFFRACTION	8	chain 'C' and (resid -1 through 7 )	C	-1 - 7
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 8 through 24 )	C	8 - 24
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 25 through 40 )	C	25 - 40
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 41 through 52 )	C	41 - 52
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 1 through 7 )	D	1 - 7
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 8 through 19 )	D	8 - 19
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 20 through 24 )	D	20 - 24
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 25 through 40 )	D	25 - 40
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 41 through 52 )	D	41 - 52
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 1 through 7 )	E	1 - 7
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 8 through 19 )	E	8 - 19
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 20 through 24 )	E	20 - 24
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 25 through 39 )	E	25 - 39
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 40 through 52 )	E	40 - 52
22	X-RAY DIFFRACTION	22	chain 'F' and (resid -2 through 7 )	F	-2 - 7
23	X-RAY DIFFRACTION	23	chain 'F' and (resid 8 through 19 )	F	8 - 19
24	X-RAY DIFFRACTION	24	chain 'F' and (resid 20 through 24 )	F	20 - 24
25	X-RAY DIFFRACTION	25	chain 'F' and (resid 25 through 42 )	F	25 - 42

-
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://pdbjlvh1.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

-
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

-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

-
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