PDB-6ey4: Periplasmic domain (residues 36-513) of GldM

ID or keywords:

Entry

Database: PDB / ID: 6ey4

Title

Periplasmic domain (residues 36-513) of GldM

Components

GldM

Keywords

PROTEIN TRANSPORT / Type IV Secretion System (T9SS)

Function / homology

Function and homology information

membrane
Similarity search - Function

Biological species

Flavobacterium johnsoniae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2 Å

Authors

Leone, P. / Roche, J. / Cambillau, C. / Roussel, A.

Funding support

France, 2items

Citation

Journal: Nat Commun / Year: 2018
Title: Type IX secretion system PorM and gliding machinery GldM form arches spanning the periplasmic space.
Authors: Leone, P. / Roche, J. / Vincent, M.S. / Tran, Q.H. / Desmyter, A. / Cascales, E. / Kellenberger, C. / Cambillau, C. / Roussel, A.

History

Deposition	Nov 10, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 7, 2018	Provider: repository / Type: Initial release
Revision 1.1	Feb 14, 2018	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2	May 8, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6ey4.cif.gz	207.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6ey4.ent.gz	166.3 KB	Display	PDB format
PDBx/mmJSON format	6ey4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6ey4_validation.pdf.gz	437.8 KB	Display	wwPDB validaton report
Full document	6ey4_full_validation.pdf.gz	439.8 KB	Display
Data in XML	6ey4_validation.xml.gz	21.2 KB	Display
Data in CIF	6ey4_validation.cif.gz	31.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ey/6ey4 ftp://data.pdbj.org/pub/pdb/validation_reports/ey/6ey4	HTTPS FTP

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Related structure data

Related structure data	6ey0C 6ey5C 6ey6C C: citing same article (ref.)
Similar structure data	5f3h-2 5jhl-d 5f3b-d 5f3h-1 5ca8-d 4qci-d 6obv-d 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

A: GldM

hetero molecules

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

1

A: GldM

hetero molecules

A: GldM

hetero molecules

defined by author&software
Evidence: assay for oligomerization, dimerization confirmed by SEC-MALS and bacterial two-hybrid on isolated domains
108 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	71.377, 71.377, 426.941
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	181
Space group name H-M	P6₄22

#1: Protein	GldM Mass: 53615.512 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: gldM / Production host: Escherichia coli (E. coli) / References: UniProt: Q5EGM3
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 297 / 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: 2.93 Å³/Da / Density % sol: 57.99 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M Hepes pH7.0-8.0 26-46%(w/v) PEG 600 / PH range: 7.0 - 8.0

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SOLEIL

/ Beamline: PROXIMA 1 / Wavelength: 0.97908 , 0.9677

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 12, 2017

Radiation

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

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97908	1
2	0.9677	1

Reflection

Resolution: 2→46.66 Å / Num. obs: 45389 / % possible obs: 100 % / Redundancy: 13.6 % / B_iso Wilson estimate: 49.72 Å² / R_rim(I) all: 0.125 / Net I/σ(I): 10.1

Reflection shell

Resolution: 2→2.11 Å / Redundancy: 14.4 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 6440 / CC_1/2: 0.667 / R_pim(I) all: 0.694 / R_rim(I) all: 2.66 / % possible all: 100

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Processing

Software

Name	Version	Classification
BUSTER	2.10.3	refinement
XDS		data reduction
SCALA		data scaling
autoSHARP		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2→43.42 Å / Cor.coef. F_o:F_c: 0.942 / Cor.coef. F_o:F_c free: 0.932 / SU R Cruickshank DPI: 0.163 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.176 / SU R_free Blow DPI: 0.159 / SU R_free Cruickshank DPI: 0.153

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.259	2277	5.03 %	RANDOM
R_work	0.222	-	-	-
obs	0.224	45243	99.9 %	-

Displacement parameters

B_iso mean: 69.64 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-6.4393 Å²	0 Å²	0 Å²
2-	-	-6.4393 Å²	0 Å²
3-	-	-	12.8785 Å²

Refine analyze

Luzzati coordinate error obs: 0.33 Å

Refinement step

Cycle: 1 / Resolution: 2→43.42 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3634	0	24	298	3956

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.009	3714	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	1.16	5000	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d		1295	SINUSOIDAL	2
X-RAY DIFFRACTION	t_incorr_chiral_ct
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_trig_c_planes
X-RAY DIFFRACTION	t_gen_planes		628	HARMONIC	5
X-RAY DIFFRACTION	t_it		3714	HARMONIC	20
X-RAY DIFFRACTION	t_nbd
X-RAY DIFFRACTION	t_omega_torsion	3.08
X-RAY DIFFRACTION	t_other_torsion	16.93
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_chiral_improper_torsion		494	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_sum_occupancies
X-RAY DIFFRACTION	t_utility_distance
X-RAY DIFFRACTION	t_utility_angle
X-RAY DIFFRACTION	t_utility_torsion
X-RAY DIFFRACTION	t_ideal_dist_contact		4278	SEMIHARMONIC	4

LS refinement shell

Resolution: 2→2.05 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.2365	166	5.13 %
R_work	0.2394	3069	-
all	0.2392	3235	-
obs	-	-	99.54 %

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	0.1488	0.7658	3.3869	1.0578	2.0351	6.1116	-0.0891	-0.2637	0.1083	0.2754	0.1335	-0.2701	0.2204	0.3494	-0.0444	0.0514	0.0287	-0.0422	0.0938	-0.0462	-0.2076	24.949	-26.3674	104.213
2	-0.0515	0.2466	3.0071	0.3019	-1.471	6.8937	-0.0128	0.2017	0.0407	-0.2771	0.1166	0.2355	-0.5077	-0.0009	-0.1038	0.1329	-0.2676	0.0325	-0.0619	-0.045	-0.2151	18.4468	-18.4124	79.9168
3	-0.5802	1.027	-0.0974	4.2356	1.9483	3.1602	-0.1171	-0.225	0.0464	0.1597	0.3468	-0.2217	-0.3524	0.2129	-0.2298	-0.0214	-0.1703	0.0724	0.0204	-0.1098	-0.1701	20.738	-14.6433	109.82
4	5.4693	-1.1094	1.5987	-2.2619	3.3563	1.2514	-0.0015	-0.1291	0.2421	0.1063	0.0966	-0.3343	0.0125	-0.1009	-0.0951	0.0582	0.0552	-0.0295	0.27	-0.0404	-0.1288	32.4118	-21.8365	118.294
5	3.617	-0.7168	-4.368	-0.864	1.3047	0.4017	0.0814	-0.1739	0.0532	0.1864	-0.0531	0.027	-0.0199	-0.1783	-0.0283	0.113	-0.1756	0.0123	0.1609	-0.133	-0.2244	16.5717	-16.4611	123.086
6	2.7027	0.1434	1.44	1.8681	0.3636	2.7126	-0.0363	-0.2557	0.185	0.1198	0.2877	0.5639	-0.4256	-0.6354	-0.2514	-0.1837	0.05	0.0872	0.0425	0.0149	-0.2454	6.2417	-13.6525	105.373
7	3.7513	-0.7732	-2.914	0.3542	0.1499	0.0051	-0.0668	-0.1943	-0.144	-0.3702	0.2802	0.5078	0.1289	-0.5848	-0.2134	0.0236	-0.439	-0.0301	0.1485	0.0396	-0.3266	5.3922	-25.6623	95.1034
8	1.0643	3.5287	3.7319	4.437	0.922	0	-0.0828	-0.3274	0.114	0.6643	0.1561	0.087	-0.2559	-0.2063	-0.0733	-0.138	-0.1134	0.1567	0.3744	-0.0163	-0.2632	3.7212	-23.6481	117.25
9	0.713	0.1455	0.1119	-0.0697	3.6141	4.627	0.0373	-0.1162	-0.022	-0.0428	0.1112	-0.0483	0.2214	-0.2373	-0.1485	0.2523	-0.2413	0.0104	-0.2021	0.0053	-0.2649	15.5391	-26.6502	86.8959
10	2.7064	2.7059	-4.4469	8.1168	6.0668	1.4972	0.5828	0.4287	0.4273	-1.2167	-0.6463	-0.6443	0.9583	0.4127	0.0634	0.0843	-0.1761	0.0283	-0.1212	0.0039	-0.1586	17.3929	-38.1149	41.6942
11	1.3704	1.6999	-0.15	2.463	-1.0578	3.7849	-0.0423	0.0668	0.1598	-0.1451	0.1893	-0.0283	-0.436	-0.3856	-0.1471	0.1382	-0.205	0.0074	-0.0186	-0.0235	-0.121	19.0209	-19.2919	55.6682
12	4.8656	0.912	-4.1386	2.727	-2.065	0.842	0.3578	-0.2027	0.111	0.1174	-0.22	-0.0462	0.1834	0.7224	-0.1378	-0.0069	-0.2255	-0.0006	-0.0381	-0.022	-0.2095	29.3507	-23.8533	55.5814
13	0.1367	-0.0789	2.3399	-0.1367	-0.7178	5.6665	-0.0314	-0.0881	-0.0382	0.0823	-0.0004	0.0307	-0.2007	-0.051	0.0318	-0.065	-0.0486	-0.0143	0.1629	-0.0246	-0.2156	20.962	-26.4149	25.8581
14	3.3201	-0.7016	0.3121	1.2654	-0.8021	6.862	-0.0488	-0.586	-0.1543	0.0704	0.1076	0.0564	0.3245	0.7674	-0.0588	-0.1404	-0.0173	0.0015	0.0654	-0.0049	-0.1995	27.0233	-36.9671	5.7977
15	3.0367	-0.0316	2.0689	1.0848	-0.8185	5.895	0.1392	-0.4448	-0.3803	0.1823	0.0914	0.0781	0.4005	-0.2315	-0.2305	0.0185	-0.039	0.018	-0.0282	0.0551	-0.1354	21.2151	-42.3605	6.7332
16	2.1665	-0.543	0.8784	0.7928	-0.0298	1.5798	-0.0874	0.3692	0.1592	0.0882	0.051	-0.2358	-0.4045	0.5428	0.0364	-0.019	-0.2532	0.0106	0.1434	0.0329	-0.1104	25.9908	-25.6585	-31.4303
17	-0.0459	0.2647	2.6533	2.0996	-2.3182	7.1362	-0.2237	0.7191	0.083	0.1487	0.2818	-0.2907	-0.076	0.4517	-0.0581	-0.1936	-0.0628	-0.0049	0.2491	0.0709	-0.2197	29.573	-29.575	-22.7834
18	1.885	-0.5937	-2.5424	1.8956	1.3592	5.9833	-0.0278	0.2214	0.1179	-0.275	-0.0308	-0.1566	0.0303	0.3537	0.0587	-0.1219	0.0663	-0.0212	0.256	-0.089	-0.3079	28.2429	-37.4891	-37.942
19	0.592	1.7187	-1.5118	2.3027	1.6755	8.0279	0.0346	0.72	-0.0662	-0.6626	0.021	-0.1458	0.1776	0.6439	-0.0555	-0.1203	0.0009	0.0555	0.3706	-0.0073	-0.3448	27.0152	-32.2713	-42.5519
20	3.5175	-1.2057	1.4744	0.0956	1.0049	7.8744	-0.0939	0.0501	-0.0424	0.1739	0.302	-0.2057	0.2193	0.5223	-0.2081	-0.1143	-0.0529	-0.0531	-0.0275	-0.0241	-0.1863	26.3418	-34.964	-26.0023

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	{ A\|-5 - 61 }
2	X-RAY DIFFRACTION	2	{ A\|62 - 85 }
3	X-RAY DIFFRACTION	3	{ A\|86 - 107 }
4	X-RAY DIFFRACTION	4	{ A\|108 - 116 }
5	X-RAY DIFFRACTION	5	{ A\|117 - 126 }
6	X-RAY DIFFRACTION	6	{ A\|127 - 156 }
7	X-RAY DIFFRACTION	7	{ A\|157 - 176 }
8	X-RAY DIFFRACTION	8	{ A\|177 - 197 }
9	X-RAY DIFFRACTION	9	{ A\|198 - 240 }
10	X-RAY DIFFRACTION	10	{ A\|241 - 260 }
11	X-RAY DIFFRACTION	11	{ A\|261 - 289 }
12	X-RAY DIFFRACTION	12	{ A\|290 - 311 }
13	X-RAY DIFFRACTION	13	{ A\|312 - 332 }
14	X-RAY DIFFRACTION	14	{ A\|333 - 373 }
15	X-RAY DIFFRACTION	15	{ A\|374 - 407 }
16	X-RAY DIFFRACTION	16	{ A\|408 - 426 }
17	X-RAY DIFFRACTION	17	{ A\|427 - 447 }
18	X-RAY DIFFRACTION	18	{ A\|448 - 468 }
19	X-RAY DIFFRACTION	19	{ A\|469 - 490 }
20	X-RAY DIFFRACTION	20	{ A\|491 - 513 }

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