PDB-3ezj: Crystal structure of the N-terminal domain of the secretin GspD f...

ID or keywords:

Entry

Database: PDB / ID: 3ezj

Title

Crystal structure of the N-terminal domain of the secretin GspD from ETEC determined with the assistance of a nanobody

Components

General secretion pathway protein GspD
NANOBODY NBGSPD_7

Keywords

PROTEIN TRANSPORT / GENERAL SECRETORY PATHWAY /

SECRETIN / SINGLE CHAIN ANTIBODY /

IMMUNE SYSTEM /

COMPLEX

Function / homology

Function and homology information

protein secretion by the type II secretion system /

type II protein secretion system complex / cell outer membrane / membrane => GO:0016020
Similarity search - Function

Biological species

Escherichia coli (E. coli)

LAMA GLAMA (llama)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.8 Å

Authors

Korotkov, K.V. / Pardon, E. / Steyaert, J. / Hol, W.G.

Citation

Journal: Structure / Year: 2009
Title: Crystal structure of the N-terminal domain of the secretin GspD from ETEC determined with the assistance of a nanobody.
Authors: Korotkov, K.V. / Pardon, E. / Steyaert, J. / Hol, W.G.

History

Deposition	Oct 22, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 17, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Jan 24, 2018	Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3	Oct 20, 2021	Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Dec 27, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ez/3ezj ftp://data.pdbj.org/pub/pdb/validation_reports/ez/3ezj	HTTPS FTP

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Related structure data

Similar structure data	5ldj-d 3t5i-d 7kkn-d 4tza-d 6l5d-d 5dn2-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) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#211 - Jul 2017 Pilus Machine similarity (6) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: General secretion pathway protein GspD

C: General secretion pathway protein GspD

E: General secretion pathway protein GspD

G: General secretion pathway protein GspD

B: NANOBODY NBGSPD_7

D: NANOBODY NBGSPD_7

F: NANOBODY NBGSPD_7

H: NANOBODY NBGSPD_7

hetero molecules

161 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: General secretion pathway protein GspD

B: NANOBODY NBGSPD_7

hetero molecules

E: General secretion pathway protein GspD

F: NANOBODY NBGSPD_7

hetero molecules

defined by software
80.4 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: General secretion pathway protein GspD

E: General secretion pathway protein GspD

B: NANOBODY NBGSPD_7

F: NANOBODY NBGSPD_7

hetero molecules

defined by software
80.4 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: General secretion pathway protein GspD

D: NANOBODY NBGSPD_7

hetero molecules

G: General secretion pathway protein GspD

H: NANOBODY NBGSPD_7

hetero molecules

defined by software
80.4 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

C: General secretion pathway protein GspD

G: General secretion pathway protein GspD

D: NANOBODY NBGSPD_7

H: NANOBODY NBGSPD_7

hetero molecules

defined by software
80.4 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	98.520, 98.520, 402.100
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	C
3	1	E
4	1	G
1	2	B
2	2	D
3	2	F
4	2	H

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	4	A	8 - 35
2	1	1	4	C	8 - 35
3	1	1	4	E	8 - 35
4	1	1	4	G	8 - 35
1	2	1	4	A	42 - 71
2	2	1	4	C	42 - 71
3	2	1	4	E	42 - 71
4	2	1	4	G	42 - 71
1	3	1	4	A	79 - 82
2	3	1	4	C	79 - 82
3	3	1	4	E	79 - 82
4	3	1	4	G	79 - 82
1	4	1	4	A	104 - 130
2	4	1	4	C	104 - 130
3	4	1	4	E	104 - 130
4	4	1	4	G	104 - 130
1	5	1	4	A	137 - 172
2	5	1	4	C	137 - 172
3	5	1	4	E	137 - 172
4	5	1	4	G	137 - 172
1	1	2	4	B	1 - 120
2	1	2	4	D	1 - 120
3	1	2	4	F	1 - 120
4	1	2	4	H	1 - 120

NCS ensembles :

ID
1
2

Details

biological unit is a dodecamer, it is unknown at the moment how individual subunits are assembled in vivo

#1: Protein	General secretion pathway protein GspD Mass: 26227.707 Da / Num. of mol.: 4 / Fragment: N-terminal domain (UNP residues 40-277) / Mutation: K38A Source method: isolated from a genetically manipulated source Details: RESIDUES 1-238, SURFACE ENTROPY MUTATION K38A / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: H10407 / Gene: gspD / Plasmid: pProEX HTb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: B3IFK0, UniProt: Q707C1*PLUS
#2: Antibody	NANOBODY NBGSPD_7 Mass: 13748.146 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) LAMA GLAMA (llama) / Gene: NBGSPD_7 / Plasmid: PHEN6 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO₄
#4: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 264 / 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: 3.52 Å³/Da / Density % sol: 65.09 %
Crystal grow	Temperature: 298 K / pH: 5 Details: 1.0M NA/K PHOSPHATE, pH 5.0, vapor diffusion, sitting drop, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9791
Detector	Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 8, 2007
Radiation	Monochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9791 Å / Relative weight: 1
Reflection	Resolution: 2.4→50 Å / Num. obs: 86152 / % possible obs: 91.7 % / Observed criterion σ(I): -3 / B_iso Wilson estimate: 57.73 Å² / R_merge(I) obs: 0.086
Reflection shell	Resolution: 2.8→2.9 Å / R_merge(I) obs: 0.767 / Mean I/σ(I) obs: 2.2 / % possible all: 91.7

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Phasing

Phasing

Method:

SAD

Phasing dm

FOM : 0.7 / FOM acentric: 0.7 / FOM centric: 0.72 / Reflection: 43800 / Reflection acentric: 39357 / Reflection centric: 4443

Phasing dm shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
8.3-37.605	0.94	0.95	0.88	2204	1611	593
5.2-8.3	0.85	0.86	0.78	6472	5538	934
4.1-5.2	0.87	0.87	0.81	8149	7265	884
3.6-4.1	0.78	0.78	0.76	7869	7162	707
3.1-3.6	0.61	0.61	0.61	12618	11696	922
2.9-3.1	0.34	0.34	0.31	6488	6085	403

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
SHELX		phasing
RESOLVE	2.13	phasing
REFMAC		refinement
PDB_EXTRACT	3.006	data extraction
SHELXD		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.8→47.67 Å / Cor.coef. F_o:F_c: 0.94 / Cor.coef. F_o:F_c free: 0.908 / Occupancy max: 1 / Occupancy min: 1 / SU B: 23.406 / SU ML: 0.235 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.499 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.239	2813	5.1 %	RANDOM
R_work	0.192	-	-	-
obs	0.194	55400	97 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 50.77 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.12 Å²	-0.06 Å²	0 Å²
2-	-	-0.12 Å²	0 Å²
3-	-	-	0.18 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→47.67 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9740	0	44	264	10048

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	9880
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	6575
X-RAY DIFFRACTION	r_angle_refined_deg	1.063	1.959	13377
X-RAY DIFFRACTION	r_angle_other_deg	0.795	3.001	16023
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.581	5	1251
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.344	24.324	444
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.37	15	1730
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.752	15	88
X-RAY DIFFRACTION	r_chiral_restr	0.062	0.2	1582
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	10953
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1899
X-RAY DIFFRACTION	r_nbd_refined	0.203	0.2	1823
X-RAY DIFFRACTION	r_nbd_other	0.188	0.2	6558
X-RAY DIFFRACTION	r_nbtor_refined	0.172	0.2	4704
X-RAY DIFFRACTION	r_nbtor_other	0.081	0.2	5585
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.152	0.2	263
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.003	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.204	0.2	19
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.193	0.2	61
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.21	0.2	6
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.43	1.5	8133
X-RAY DIFFRACTION	r_mcbond_other	0.053	1.5	2587
X-RAY DIFFRACTION	r_mcangle_it	0.479	2	10151
X-RAY DIFFRACTION	r_scbond_it	0.752	3	4077
X-RAY DIFFRACTION	r_scangle_it	1.189	4.5	3226
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	1572	medium positional	0.24	0.5
1	2	C	1572	medium positional	0.25	0.5
1	3	E	1572	medium positional	0.22	0.5
1	4	G	1572	medium positional	0.22	0.5
2	1	B	1512	medium positional	0.23	0.5
2	2	D	1512	medium positional	0.3	0.5
2	3	F	1512	medium positional	0.22	0.5
2	4	H	1512	medium positional	0.22	0.5
1	1	A	1572	medium thermal	0.19	2
1	2	C	1572	medium thermal	0.22	2
1	3	E	1572	medium thermal	0.24	2
1	4	G	1572	medium thermal	0.21	2
2	1	B	1512	medium thermal	0.2	2
2	2	D	1512	medium thermal	0.21	2
2	3	F	1512	medium thermal	0.19	2
2	4	H	1512	medium thermal	0.21	2

LS refinement shell

Resolution: 2.8→2.87 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.3	200	-
R_work	0.278	3811	-
obs	-	-	97.69 %

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	3.552	-1.7862	-0.9947	11.582	2.3625	4.7011	-0.0837	-0.4423	-0.5741	0.4345	0.4945	-0.6341	0.265	0.6674	-0.4108	-0.0993	0.0007	-0.119	-0.1477	-0.0218	-0.0632	56.442	-26.822	28.606
2	2.3414	0.3127	1.767	3.5596	1.4329	5.9199	-0.2182	-0.1099	-0.1159	0.0199	0.2961	-0.0304	-0.0962	0.1299	-0.0779	0.0687	-0.0952	-0.011	-0.153	-0.0777	0.0762	48.009	-24.638	16.416
3	0.1968	0.0181	0.1745	1.3012	-3.0254	11.199	0.0291	0.4248	-0.0041	-0.0426	0.1746	0.318	0.9366	-0.4502	-0.2037	0.1709	-0.2518	0.0932	0.1133	-0.1756	0.3065	42.689	-29.098	-15.562
4	23.2621	1.7597	1.1684	8.6319	5.3168	9.8309	-0.5046	-0.5052	-1.4638	0.6858	0.3581	0.3114	2.1573	-0.0189	0.1465	0.2622	-0.2337	0.3873	-0.1153	-0.2809	0.0622	44.118	-34.029	-24.994
5	5.1779	0.0059	0.731	2.1753	-0.4373	0.9038	0.119	-0.1633	0.1731	0.5391	0.0096	0.329	-0.1333	-0.0485	-0.1286	0.1029	-0.1392	0.0951	-0.2192	0.0004	0.1062	29.759	-14.46	8.589
6	11.3924	-5.1595	3.5865	12.0573	-3.15	8.8285	-0.2032	-1.1298	-0.2777	1.4636	0.467	0.8183	-0.7124	-0.1419	-0.2638	0.0749	0.1073	0.3526	-0.0944	0.1923	-0.3001	47.844	-11.804	100.978
7	3.7154	-1.5357	1.1126	4.1338	-0.4208	4.1624	0.1924	-0.2296	-0.2497	0.4383	-0.0117	0.4041	0.1718	0.0016	-0.1807	0.0815	0.1332	0.1186	-0.1285	0.0941	-0.0546	49.623	-8.311	86.727
8	1.1271	0.2687	4.1112	0.0947	0.6948	17.6468	0.0061	-0.0529	-0.299	-0.2005	0.0541	0.1185	-0.6874	-0.5101	-0.0603	0.225	0.2855	-0.0821	0.0389	-0.01	0.3413	37.648	-6.922	55.909
9	10.8239	-2.7761	4.7072	10.0193	-7.1154	15.3859	-0.4119	-0.9504	0.1024	1.1866	0.1876	0.9721	-0.3615	-0.8345	0.2243	0.0012	0.135	-0.1101	-0.1956	-0.1153	0.2657	29.097	-7.061	49.014
10	1.4987	-0.202	-1.3155	5.254	-1.6277	2.9944	0.0337	-0.0971	0.2383	0.2286	0.0355	-0.5018	-0.0803	0.166	-0.0692	-0.0692	0.1324	0.0371	-0.124	0.039	0.0272	63.428	0.537	71.515
11	5.5715	2.043	2.3178	9.9164	3.6483	4.8332	-0.0014	0.7915	-0.332	-0.1189	0.4747	-1.2466	0.275	0.2507	-0.4732	-0.2385	-0.0711	0.1484	-0.0613	-0.2652	0.0779	70.749	-21.292	-18.476
12	2.7131	-0.5889	0.1529	5.8857	4.6611	3.9253	0.0295	0.3319	0.1337	-0.057	-0.0662	-0.0696	0.055	-0.0596	0.0367	-0.0319	-0.1324	0.0549	-0.073	-0.1139	0.124	60.877	-13.595	-10.795
13	5.0055	-1.5859	-9.4978	0.5159	3.1048	18.7018	0.2516	0.0091	0.6413	-0.1377	0.5323	0.0978	-0.4672	0.1517	-0.7839	0.5448	-0.1053	0.0371	-0.1539	-0.0911	0.3995	51.573	-0.188	18.6
14	20.4152	-3.8878	-13.9002	13.8727	-8.2006	18.4249	0.4199	-1.1599	0.202	-1.109	-0.9098	-2.5181	-1.2132	2.9828	0.4899	-0.0029	-0.1278	0.1676	-0.2423	0.0536	0.4337	55.063	5.248	29.035
15	3.6885	-1.2129	0.0044	4.7556	0.0903	0.9676	-0.1187	0.4032	0.1278	-0.1867	0.1677	0.0424	-0.0321	-0.0629	-0.049	-0.0533	-0.2188	0.0608	-0.1213	-0.0062	0.1026	42.024	-1.523	-11.623
16	9.7176	-1.661	3.2685	7.766	-0.3703	6.6136	0.1243	-0.0141	-0.836	-0.7641	0.1648	2.426	0.3272	-0.7852	-0.2891	-0.2091	-0.1116	-0.1546	-0.1629	0.0028	0.8522	29.909	-34.838	60.493
17	5.5342	-1.5522	1.1675	5.1992	-0.6709	2.4273	-0.1558	0.0812	-0.2737	-0.4194	-0.0005	0.8306	0.044	-0.2418	0.1564	-0.0271	0.096	-0.0178	-0.127	0.0312	0.1933	42.016	-28.734	62.62
18	5.7124	-0.2013	1.2979	9.3931	1.2694	2.1124	-0.3202	-0.0345	-0.5045	0.3676	0.2279	0.565	0.4736	0.0216	0.0923	0.0014	0.1118	0.0619	-0.1674	0.081	0.0483	49.981	-32.646	68.43
19	13.5347	1.6944	-0.7625	11.0026	-2.3197	2.5716	-0.4453	0.2087	-0.0255	0.31	0.4553	-0.945	-0.1378	0.2098	-0.0099	0.2445	0.328	-0.1552	-0.0175	-0.0444	0.0792	73.342	-22.381	90.682
20	4.0365	-0.6322	-0.6921	3.2511	-0.1371	0.8768	-0.0674	0.1484	-0.1636	-0.4349	-0.0405	-0.179	-0.0118	-0.0853	0.1078	0.079	0.1351	0.0676	-0.1562	0.043	-0.05	61.887	-20.24	54.411

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	4 - 47
2	X-RAY DIFFRACTION	2	A	48 - 153
3	X-RAY DIFFRACTION	3	A	154 - 209
4	X-RAY DIFFRACTION	4	A	213 - 235
5	X-RAY DIFFRACTION	5	B	1 - 120
6	X-RAY DIFFRACTION	6	C	4 - 47
7	X-RAY DIFFRACTION	7	C	48 - 153
8	X-RAY DIFFRACTION	8	C	154 - 209
9	X-RAY DIFFRACTION	9	C	214 - 235
10	X-RAY DIFFRACTION	10	D	1 - 120
11	X-RAY DIFFRACTION	11	E	4 - 47
12	X-RAY DIFFRACTION	12	E	48 - 152
13	X-RAY DIFFRACTION	13	E	153 - 217
14	X-RAY DIFFRACTION	14	E	222 - 235
15	X-RAY DIFFRACTION	15	F	1 - 120
16	X-RAY DIFFRACTION	16	G	4 - 47
17	X-RAY DIFFRACTION	17	G	48 - 126
18	X-RAY DIFFRACTION	18	G	127 - 163
19	X-RAY DIFFRACTION	19	G	164 - 235
20	X-RAY DIFFRACTION	20	H	1 - 120

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