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

ID or keywords:

Entry

Database: PDB / ID: 6hfx

Title

Crystal structure of Extracellular Domain 1 (ECD1) of FtsX from S. pneumonie in complex with n-decyl-B-D-maltoside

Components

Cell division protein FtsX

Keywords

MEMBRANE PROTEIN /

Divisome

Function / homology

Function and homology information

membrane => GO:0016020 /

cell cycle /

cell division /

plasma membrane
Similarity search - Function

Biological species

Streptococcus pneumoniae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.16 Å

Authors

Alcorlo Pages, M. / Martinez-Caballero, S.

Funding support

Spain, 1items

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 22, 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

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PDBx/mmCIF format	6hfx.cif.gz	111.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6hfx.ent.gz	87 KB	Display	PDB format
PDBx/mmJSON format	6hfx.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hf/6hfx ftp://data.pdbj.org/pub/pdb/validation_reports/hf/6hfx	HTTPS FTP

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Related structure data

Related structure data	6he6SC 6heeC 6mk7C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6he6-1 6he6-2 3x0t-1 5trb-1 2yup-d 6vfo-d 4r7e-1 2h41-1 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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

B: Cell division protein FtsX

A: Cell division protein FtsX

hetero molecules

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

1

B: Cell division protein FtsX

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

2

A: Cell division protein FtsX

hetero molecules

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

Unit cell

Length a, b, c (Å)	75.496, 75.496, 95.311
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: 13012.221 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-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A0I6INF5, UniProt: Q04LE4*PLUS
#2: Sugar	ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Formula: C₂₂H₄₂O₁₁ / Comment: detergent*YM
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.49 Å³/Da / Density % sol: 50.73 % / Description: Bipyramidal
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.1 M Sodium Citrate pH=5.6, 0.2 M Potassium-Sodium Tartrate and 2M Amonium Sulfate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979257 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 13, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979257 Å / Relative weight: 1
Reflection	Resolution: 2.16→46.58 Å / Num. obs: 28508 / % possible obs: 98.85 % / Redundancy: 16.6 % / R_merge(I) obs: 0.072 / R_pim(I) all: 0.016 / R_rim(I) all: 0.074 / Net I/σ(I): 23.1
Reflection shell	Resolution: 2.16→46.58 Å / R_merge(I) obs: 1.526 / R_pim(I) all: 0.332 / R_rim(I) all: 1.563

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6HE6

6he6

Resolution: 2.16→46.576 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 40.59

	R_factor	Num. reflection	% reflection
R_free	0.3157	1516	5.37 %
R_work	0.2596	-	-
obs	0.2626	28206	99.9 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.16→46.576 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1826	0	33	23	1882

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	1917
X-RAY DIFFRACTION	f_angle_d	1.169	2597
X-RAY DIFFRACTION	f_dihedral_angle_d	19.456	1168
X-RAY DIFFRACTION	f_chiral_restr	0.068	298
X-RAY DIFFRACTION	f_plane_restr	0.006	338

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 (%)
2.16-2.2297	0.4458	121	0.3764	2461	X-RAY DIFFRACTION	100
2.2297-2.3094	0.3637	132	0.3693	2427	X-RAY DIFFRACTION	100
2.3094-2.4019	0.4461	146	0.3477	2405	X-RAY DIFFRACTION	100
2.4019-2.5112	0.4103	156	0.3405	2423	X-RAY DIFFRACTION	100
2.5112-2.6436	0.5204	127	0.3375	2436	X-RAY DIFFRACTION	100
2.6436-2.8092	0.3605	127	0.3272	2447	X-RAY DIFFRACTION	100
2.8092-3.026	0.3673	147	0.3114	2415	X-RAY DIFFRACTION	100
3.026-3.3305	0.3295	136	0.2589	2423	X-RAY DIFFRACTION	100
3.3305-3.8122	0.3121	145	0.24	2426	X-RAY DIFFRACTION	100
3.8122-4.8022	0.2686	135	0.1938	2423	X-RAY DIFFRACTION	100
4.8022-46.5864	0.2445	144	0.2334	2404	X-RAY DIFFRACTION	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	2.2065	-0.776	0.0637	6.9799	-4.4015	2.9721	-0.292	-0.217	-0.6238	0.7027	0.9855	0.7127	-1.9836	0.6414	-0.164	0.5788	-0.1467	0.0803	0.6709	-0.1298	0.2941	-21.7394	0.2016	22.8248
2	1.3587	0.9901	2.9487	5.3664	2.8753	6.5442	0.5403	0.148	0.4335	-0.8442	-0.0802	0.458	-0.9121	0.1	-0.0615	0.7264	-0.1323	0.0393	0.5622	-0.0919	0.4547	-22.7669	4.2697	4.5337
3	3.9501	-1.8574	3.5621	4.6401	-4.5927	5.9374	0.4972	0.5965	-0.247	-0.9526	0.3308	-0.1351	0.1021	-0.1026	0.1289	0.3962	-0.0469	-0.0662	0.3818	-0.1092	0.6753	-31.4176	3.7154	-8.0468
4	2.6329	-0.5258	1.6127	3.9107	-0.8784	8.8798	0.7128	0.3631	-0.7482	-0.35	-0.0443	0.8384	0.9062	1.1053	-0.161	0.5261	0.1033	-0.1153	0.3816	-0.1283	0.5009	-23.2618	-6.1566	10.5473
5	4.0222	-1.3025	-0.8103	3.3816	3.6056	4.0201	-0.5683	-1.393	0.5819	-0.1284	-0.4392	0.3959	-0.2297	-0.989	0.1189	0.5839	-0.2678	0.1502	0.6127	-0.212	0.748	-29.5053	15.5681	18.9565
6	1.8861	2.737	-1.5434	3.8623	-2.2516	1.3387	-0.0382	0.2586	0.7701	0.0068	1.1117	-1.8801	-0.246	0.1963	-0.0032	1.2482	0.0384	0.2069	0.7367	0.1328	1.211	-25.5027	24.8611	16.2656
7	4.6596	-0.2913	1.5867	2.515	-1.535	6.8542	0.0308	0.5066	-0.1487	0.172	-0.0665	-0.3121	-0.4543	2.1004	-0.0129	0.4123	-0.1352	-0.029	0.8337	-0.167	0.4609	-16.8534	1.0541	16.0512
8	6.417	0.3131	-3.6637	1.1595	-0.0515	2.0965	-0.5415	0.8786	-0.1328	-0.8616	-0.1336	0.256	1.1383	-1.6834	-0.1182	0.7864	-0.2193	-0.0756	0.6732	0.0062	0.217	-37.3455	-16.679	-23.2939
9	6.503	5.3735	-1.1278	4.6527	-0.1647	8.5362	0.3034	-0.7077	0.9209	0.1222	-0.0794	0.6136	1.558	-0.8647	0.0831	0.7445	-0.1908	-0.0773	0.6128	0.0301	0.3634	-40.7473	-14.3942	-4.724
10	2.553	1.3515	1.5976	5.0864	4.3727	3.8863	-0.0716	-0.8699	0.2158	0.4187	0.1103	-0.1688	-0.3834	0.3884	0.1959	0.4946	-0.0511	-0.0509	0.4138	-0.1153	0.517	-41.3744	-6.1252	7.1947
11	3.2501	-0.7529	-2.9193	3.2075	2.0226	7.9166	-0.3227	-0.6379	0.4407	0.2235	0.6127	-0.1957	1.0825	0.9087	-0.1105	0.3471	0.0763	-0.0116	0.4671	-0.0659	0.3749	-31.5367	-14.0655	-11.1145
12	4.1138	-1.3001	3.4996	0.7674	-0.9436	3.6881	-0.4877	-0.3679	0.1022	-0.229	-0.0261	-0.8439	-0.4368	0.2665	0.1431	0.4365	-0.1227	0.0485	0.6551	0.0529	0.7218	-51.0949	-10.2331	-20.3424
13	5.6848	3.4465	0.4974	2.1558	0.5778	4.2848	-0.2587	-0.7412	0.6888	0.0179	-0.4119	0.4341	-0.5162	-0.1395	0.1784	0.563	-0.1026	-0.0402	0.6453	0.0455	0.4452	-57.1267	-13.7844	-15.0869
14	2.7343	-2.8978	-1.6562	3.1468	0.9304	7.1727	-0.6349	-0.0177	-0.6013	-0.0248	0.4177	0.2041	2.1648	-0.1364	0.0889	0.9144	-0.093	-0.0085	0.4099	0.0009	0.4604	-33.729	-22.7347	-17.771

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 52 through 64 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 65 through 73 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 74 through 83 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 84 through 106 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 107 through 122 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 123 through 127 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 128 through 165 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 52 through 64 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 65 through 73 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 74 through 83 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 84 through 107 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 108 through 119 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 120 through 135 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 136 through 165 )

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