PDB-8v7q: IpaD (122-321) Pi-helix Mutant (delta Q148) Apo Structure

ID or keywords:

Entry

Database: PDB / ID: 8v7q

Title

IpaD (122-321) Pi-helix Mutant (delta Q148) Apo Structure

Components

Invasin IpaD

Keywords

CELL INVASION / Type Three Secretion System / T3SS / T3SA / Shigella / Pi helix

Function / homology

effector-mediated activation of host programmed cell death by symbiont / Type III secretion systems tip complex components / BipD-like superfamily / Type III secretion systems tip complex components / extracellular region / Invasin IpaD

Function and homology information

Biological species

Shigella flexneri (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3 Å

Authors

Barker, S.A. / Dickenson, N.E. / Johnson, S.J.

Funding support

United States, 1items

Citation

Journal: J.Biol.Chem. / Year: 2024
Title: Structural and functional characterization of the IpaD pi-helix reveals critical roles in DOC interaction, T3SS apparatus maturation, and Shigella virulence.
Authors: Barker, S.A. / Bernard, A.R. / Morales, Y. / Johnson, S.J. / Dickenson, N.E.

History

Deposition	Dec 4, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 21, 2024	Provider: repository / Type: Initial release
Revision 1.1	Sep 18, 2024	Group: Database references / Category: citation / Item: _citation.journal_volume

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8v7q.cif.gz	310 KB	Display	PDBx/mmCIF format
PDB format	pdb8v7q.ent.gz	256.9 KB	Display	PDB format
PDBx/mmJSON format	8v7q.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8v7q_validation.pdf.gz	443.9 KB	Display	wwPDB validaton report
Full document	8v7q_full_validation.pdf.gz	446.4 KB	Display
Data in XML	8v7q_validation.xml.gz	26.3 KB	Display
Data in CIF	8v7q_validation.cif.gz	34.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v7/8v7q ftp://data.pdbj.org/pub/pdb/validation_reports/v7/8v7q	HTTPS FTP

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Related structure data

Related structure data	8v5cC 8v5eC 8v7sC C: citing same article (ref.)
Similar structure data	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: Invasin IpaD

B: Invasin IpaD

C: Invasin IpaD

D: Invasin IpaD

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

1

A: Invasin IpaD

C: Invasin IpaD

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

2

B: Invasin IpaD

D: Invasin IpaD

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

Unit cell

Length a, b, c (Å)	44.962, 69.422, 172.958
Angle α, β, γ (deg.)	90.00, 90.28, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Invasin IpaD Mass: 21853.375 Da / Num. of mol.: 4 / Mutation: Q148 deleted Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: ipaD / Production host: Escherichia coli (E. coli) / References: UniProt: P18013

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.09 Å³/Da / Density % sol: 60.17 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M HEPES pH 7.5, 0.018 - 0.02 M Magnesium Chloride Hexahydrate, 20% w/v Poly(acrylic acid sodium salt) 5100

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Data collection

Diffraction

Mean temperature: 80 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL9-2 / Wavelength: 0.97946 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2021

Radiation

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

Radiation wavelength

Wavelength: 0.97946 Å / Relative weight: 1

Reflection

Resolution: 3→50 Å / Num. obs: 21120 / % possible obs: 95.8 % / Redundancy: 6.2 % / R_merge(I) obs: 0.074 / R_pim(I) all: 0.031 / R_rim(I) all: 0.08 / Χ²: 1 / Net I/σ(I): 11.6

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
3-3.11	4.1	1.04	1875	0.602	0.867	0.538	1.178	1.005	86.4
3.11-3.23	5.3	0.705	2063	0.757	0.928	0.324	0.779	1.002	95.1
3.23-3.38	6.2	0.451	2124	0.908	0.976	0.191	0.491	0.997	97.7
3.38-3.56	6.5	0.271	2170	0.972	0.993	0.113	0.295	0.995	98.1
3.56-3.78	6.7	0.194	2176	0.979	0.995	0.08	0.21	0.996	98.2
3.78-4.07	6.1	0.151	2036	0.99	0.998	0.065	0.165	0.997	93.4
4.07-4.48	6.6	0.081	2092	0.997	0.999	0.034	0.088	1.003	95.4
4.48-5.13	7	0.063	2190	0.998	0.999	0.026	0.068	1.002	98.6
5.13-6.46	6.8	0.056	2188	0.999	1	0.023	0.061	1.003	98.2
6.46-50	6.5	0.031	2206	1	1	0.013	0.033	1.003	97.1

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Processing

Software

Name	Version	Classification
PHENIX	1.14_3260	refinement
HKL-3000		data scaling
HKL-3000		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3→29.737 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.7 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2708	1031	4.99 %
R_work	0.2568	-	-
obs	0.2575	20672	95.89 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 3→29.737 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6000	0	0	0	6000

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	6096
X-RAY DIFFRACTION	f_angle_d	0.408	8245
X-RAY DIFFRACTION	f_dihedral_angle_d	1.723	3681
X-RAY DIFFRACTION	f_chiral_restr	0.034	926
X-RAY DIFFRACTION	f_plane_restr	0.003	1059

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 (%)
3-3.158	0.3608	136	0.3858	2651	X-RAY DIFFRACTION	92
3.158-3.3556	0.3627	145	0.3583	2777	X-RAY DIFFRACTION	97
3.3556-3.6143	0.3457	149	0.3205	2870	X-RAY DIFFRACTION	98
3.6143-3.9772	0.2879	147	0.2965	2785	X-RAY DIFFRACTION	95
3.9772-4.551	0.2851	142	0.2502	2764	X-RAY DIFFRACTION	94
4.551-5.7271	0.2804	154	0.24	2866	X-RAY DIFFRACTION	98
5.7271-29.737	0.2044	158	0.1967	2928	X-RAY DIFFRACTION	98

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	1.7577	0.6115	1.1934	3.9042	4.4596	5.4395	0.0717	0.0768	-0.3487	0.9615	0.361	-0.4335	1.2828	0.4323	-0.4337	0.7206	0.0996	-0.1244	0.687	-0.0202	0.7217	-1.7506	-4.4367	28.7848
2	1.7194	1.7086	1.7628	4.2332	3.9346	4.438	-0.0035	0.2493	-0.4237	-0.2288	0.2522	-0.2754	0.1671	0.4159	-0.2331	0.6356	0.1568	-0.0984	0.6686	-0.1176	0.7294	-5.7876	-5.1177	18.628
3	1.5642	0.3261	-0.808	0.5635	-0.354	4.7341	-0.0825	0.269	-0.4326	0.1849	-0.0258	-0.0512	0.3315	-0.2067	0.1196	0.7776	-0.0364	0.0485	0.4832	-0.0499	0.5407	-42.1672	17.243	62.7991
4	3.8725	-0.5119	-2.921	4.6333	0.8962	5.541	-0.2357	-0.2559	-0.1776	0.2912	0.0401	-0.3299	0.8924	0.1035	0.2308	0.5837	0.0232	0.0653	0.4876	0.1458	0.5689	-41.885	11.3154	82.6444
5	3.7096	-0.2879	-1.612	0.5721	0.2964	6.7565	-0.1558	-0.0846	0.0014	0.2678	-0.2538	-0.3331	-0.1164	0.7012	0.4037	0.6863	-0.0841	-0.058	0.5149	0.0064	0.7356	-38.9531	23.6996	77.1445
6	2.2479	0.4136	2.7695	1.0814	0.4951	4.8738	-0.2344	-0.4645	0.4696	-0.101	-0.1813	0.0282	-0.4574	-0.7508	0.4729	0.7571	0.0826	-0.0341	0.6185	-0.0541	0.5519	-19.4704	21.4415	23.729
7	4.8758	-0.4722	0.0512	4.5812	-1.2017	8.3337	-0.6149	0.2433	0.2767	-0.0864	0.2219	0.5485	-1.1318	-0.913	-0.1118	0.8483	-0.0461	-0.1079	0.6495	0.2574	0.7013	-26.3832	22.8138	-8.6341
8	2.585	-0.0869	2.3266	0.956	-1.6842	5.8031	-0.2794	0.4107	0.1631	0.0165	-0.1147	-0.4082	-0.5259	0.4275	0.3575	0.5531	0.021	-0.0263	0.7325	0.0517	0.6904	-16.1628	22.477	9.9169
9	2.0884	-0.7305	-1.8771	2.9575	2.2934	2.5991	0.1487	-0.183	0.2053	-0.2735	1.162	-1.3007	-0.2349	1.1717	-0.9239	0.5036	-0.0615	0.0522	0.791	-0.1764	0.7186	-23.9869	36.7884	58.1383
10	3.517	-1.0348	-0.0255	5.3621	1.5771	2.8795	0.7668	0.6047	0.9713	-1.423	-0.2974	-0.5954	-1.9428	0.0913	-0.3219	1.0847	-0.0242	0.2959	0.7481	0.0056	0.8281	-25.1076	51.007	57.1954
11	1.4429	-2.103	-2.1177	3.2117	3.8541	6.3223	-0.2211	-0.0988	0.1734	0.4653	-0.1334	0.3715	-0.0061	0.1877	0.2944	0.4834	-0.1053	0.0922	0.7921	-0.1583	0.7452	-28.5788	42.9843	69.2042

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 124 through 242 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 243 through 319 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 124 through 179 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 180 through 261 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 262 through 319 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 124 through 179 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 180 through 204 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 205 through 319 )
9	X-RAY DIFFRACTION	9	chain 'D' and (resid 124 through 190 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 191 through 249 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 250 through 319 )

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