PDB-6he6: Crystal structure of Extracellular Domain 1 (ECD1) of FtsX from S...

ID or keywords:

Entry

Database: PDB / ID: 6he6

Title

Crystal structure of Extracellular Domain 1 (ECD1) of FtsX from S. pneumonie in complex with dodecane-trimethylamine

Components

Cell division protein FtsX

Keywords

CELL CYCLE / cell division / MEMBRANE PROTEIN

Function / homology

Function and homology information

cell cycle / membrane => GO:0016020 / cell division / plasma membrane
Similarity search - Function

Biological species

Streptococcus pneumoniae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Martinez-Caballero, S. / Alcorlo-Pages, M. / Hermoso, J.A.

Citation

Journal: Mbio / Year: 2019
Title: Structure of the Large Extracellular Loop of FtsX and Its Interaction with the Essential Peptidoglycan Hydrolase PcsB in Streptococcus pneumoniae.
Authors: Rued, B.E. / Alcorlo, M. / Edmonds, K.A. / Martinez-Caballero, S. / Straume, D. / Fu, Y. / Bruce, K.E. / Wu, H. / Havarstein, L.S. / Hermoso, J.A. / Winkler, M.E. / Giedroc, D.P.

History

Deposition	Aug 20, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 24, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jan 17, 2024	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	6he6.cif.gz	110.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6he6.ent.gz	86 KB	Display	PDB format
PDBx/mmJSON format	6he6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6he6_validation.pdf.gz	444.5 KB	Display	wwPDB validaton report
Full document	6he6_full_validation.pdf.gz	448.5 KB	Display
Data in XML	6he6_validation.xml.gz	11.4 KB	Display
Data in CIF	6he6_validation.cif.gz	14.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/he/6he6 ftp://data.pdbj.org/pub/pdb/validation_reports/he/6he6	HTTPS FTP

-
Related structure data

Related structure data	6heeC 6hfxC 6mk7C 4n8nS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6hfx-1 6hfx-2 2lpe-d 6vfo-d 4esk-2 5z8i-d 4esk-1 1f9x-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

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Cell division protein FtsX

B: Cell division protein FtsX

hetero molecules

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

1

A: Cell division protein FtsX

hetero molecules

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

2

B: Cell division protein FtsX

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

Unit cell

Length a, b, c (Å)	75.870, 75.870, 97.928
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

#1: Protein	Cell division protein FtsX Mass: 13325.637 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: ERS044004_00806 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0I6INF5, UniProt: Q04LE4*PLUS
#2: Chemical	ChemComp-CAT / DODECANE-TRIMETHYLAMINE Mass: 228.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₅H₃₄N
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.64 Å³/Da / Density % sol: 53.48 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: ammonium sulfate, sodium and potassium tartrate and sodium citrate

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97934 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 13, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97934 Å / Relative weight: 1
Reflection	Resolution: 2→47.05 Å / Num. obs: 19939 / % possible obs: 96.69 % / Redundancy: 24.4 % / R_pim(I) all: 0.006 / Net I/σ(I): 23.12
Reflection shell	Resolution: 2→2.05 Å / R_pim(I) all: 0.444

-
Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: ???)	refinement
XDS		data reduction
Aimless		data scaling
MoRDa		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4N8N

4n8n

Resolution: 2→47.05 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 35.86

	R_factor	Num. reflection	% reflection
R_free	0.2819	951	4.78 %
R_work	0.2411	-	-
obs	0.2431	19881	99.7 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2→47.05 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1870	0	16	25	1911

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	1929
X-RAY DIFFRACTION	f_angle_d	0.889	2609
X-RAY DIFFRACTION	f_dihedral_angle_d	6.134	1651
X-RAY DIFFRACTION	f_chiral_restr	0.058	294
X-RAY DIFFRACTION	f_plane_restr	0.004	342

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 (%)
2-2.1055	0.4113	129	0.3695	2666	X-RAY DIFFRACTION	100
2.1055-2.2374	0.4149	147	0.3259	2617	X-RAY DIFFRACTION	100
2.2374-2.4101	0.3795	126	0.3283	2629	X-RAY DIFFRACTION	99
2.4101-2.6527	0.3266	143	0.2981	2679	X-RAY DIFFRACTION	100
2.6527-3.0365	0.3281	138	0.2956	2708	X-RAY DIFFRACTION	100
3.0365-3.8254	0.2655	129	0.2444	2740	X-RAY DIFFRACTION	100
3.8254-47.0634	0.2448	139	0.1963	2891	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	0.5976	0.6759	0.0104	0.7505	0.0607	0.0223	0.8523	-0.3588	0.524	-0.5025	1.0871	-0.9388	0.1578	-1.1726	0.0316	1.7197	-0.1899	-0.2067	1.1965	0.1807	1.3976	29.4838	2.0453	28.6974
2	1.0585	-0.1607	0.5198	2.6972	-0.6517	0.7802	-0.0739	0.0245	-0.2971	0.1959	0.2512	-0.3929	0.923	-0.3012	0.0008	0.5904	-0.0241	-0.0869	0.6163	-0.0323	0.5301	21.1909	-1.7244	13.9753
3	0.2263	-0.4041	0.5275	0.0174	-0.0007	0.5261	0.0387	-0.0211	0.3992	-0.4156	0.0607	-0.1801	-0.3025	-0.1925	0.0001	0.517	0.0353	0.0852	0.5814	-0.0973	0.7176	30.0343	-0.8141	-2.706
4	0.8487	0.9132	-0.2813	0.6934	0.1738	1.5032	0.533	0.0711	0.2266	-0.2927	-0.0764	-0.6935	-0.3442	-0.5155	0.0001	0.5734	0.1189	-0.0063	0.4538	-0.0197	0.4698	23.2414	7.0079	15.4069
5	0.4861	-0.5271	-0.052	0.332	-0.076	0.1039	-0.2143	-0.1028	0.4305	-0.5601	-0.9924	-0.4609	0.4618	-0.5778	-0.0032	0.614	-0.1287	-0.0806	0.5355	0.0615	0.6788	28.1262	-13.2515	20.4257
6	0.4444	0.4927	0.7221	0.2182	0.4089	0.5811	-0.2408	-0.2658	0.3399	0.4016	-0.2444	-0.5596	0.1816	0.3413	-0.0021	0.7646	-0.1508	0.0325	0.6415	0.0033	0.4936	24.3922	-19.6969	16.539
7	1.5942	-0.4264	-0.3238	1.9201	-0.5082	1.1249	0.4213	0.0867	-0.031	0.0094	-0.0874	0.0518	-0.0135	-1.2693	-0.0008	0.5154	0.0734	-0.0923	0.7975	-0.0029	0.4394	15.061	4.1928	18.4184
8	0.1186	0.1261	-0.0848	0.2552	-0.0459	0.0095	-0.0322	0.3353	0.8294	0.3258	0.5772	-0.3915	-0.4722	-0.8642	-0.0024	0.9473	-0.0663	-0.1077	1.0972	0.1019	0.9717	40.0688	-7.6465	20.8229
9	1.8145	-0.5741	-0.0047	1.2379	-0.065	0.7795	0.089	0.2371	0.1924	0.4687	-0.1702	0.124	0.6319	-0.8133	0.0011	0.5578	-0.1013	-0.0099	0.5811	0.0228	0.4093	35.6914	-16.1662	35.6026
10	0.1166	-0.0708	-0.5226	0.3981	0.9056	1.5278	0.1328	0.051	0.5503	0.3087	0.355	-0.2425	0.1979	0.4502	-0.0013	0.4424	0.0389	-0.004	0.5614	-0.023	0.541	41.2176	-11.6502	42.4106
11	0.274	0.1175	-0.2225	0.404	-0.1031	0.2438	-0.4962	-0.7949	2.0115	0.2141	0.5598	0.9065	-0.595	-0.4711	0.0156	0.4653	0.0102	-0.0126	0.7124	0.2949	0.998	24.3614	-8.3338	31.1481
12	0.2872	0.1664	0.7267	0.0809	0.3788	1.7116	1.1954	-0.5875	0.8926	-0.0715	-0.5438	-1.2617	-1.8609	-1.8731	0.0077	0.9962	0.0343	0.1583	0.8622	-0.1078	1.2119	14.3598	-10.3801	28.9761
13	0.6703	0.7395	0.6664	0.9676	1.2852	1.2198	-0.3284	-0.0206	-0.0526	0.2165	-0.0221	0.1918	0.5097	-0.2113	0.0003	0.3915	-0.0327	0.0545	0.5781	0.1291	0.523	32.5631	-15.156	32.9263
14	0.9991	0.5825	-0.0831	1.2752	0.1225	0.0188	-0.8823	0.0085	-0.8813	0.1577	0.26	-0.0508	2.1001	-0.1976	-0.0158	1.0507	0.0193	0.0159	0.5404	0.0574	0.5341	40.9803	-25.0237	32.003

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 8 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 9 through 26 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 27 through 41 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 42 through 60 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 61 through 71 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 72 through 88 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 89 through 118 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 2 through 8 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 9 through 26 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 27 through 60 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 61 through 70 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 71 through 80 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 81 through 96 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 97 through 118 )

-
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

-
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