PDB-3gr0: Periplasmic domain of the T3SS inner membrane protein PrgH from S...

ID or keywords:

Entry

Database: PDB / ID: 3gr0

Title

Periplasmic domain of the T3SS inner membrane protein PrgH from S.typhimurium (fragment 170-362)

Components

Protein prgH

Keywords

MEMBRANE PROTEIN / Type III secretion system / inner membrane protein / Cell membrane / Membrane / Transmembrane / Virulence

Function / homology

Function and homology information

plasma membrane
Similarity search - Function

Biological species

Salmonella typhimurium (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.3 Å

Authors

Yip, C.K. / Vockovic, M. / Yu, A.C. / Strynadka, N.C.J.

Citation

Journal: Nat.Struct.Mol.Biol. / Year: 2009
Title: A conserved structural motif mediates formation of the periplasmic rings in the type III secretion system.
Authors: Spreter, T. / Yip, C.K. / Sanowar, S. / Andre, I. / Kimbrough, T.G. / Vuckovic, M. / Pfuetzner, R.A. / Deng, W. / Yu, A.C. / Finlay, B.B. / Baker, D. / Miller, S.I. / Strynadka, N.C.

History

Deposition	Mar 24, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 19, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Feb 21, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3gr0.cif.gz	161.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3gr0.ent.gz	130.8 KB	Display	PDB format
PDBx/mmJSON format	3gr0.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3gr0_validation.pdf.gz	446.2 KB	Display	wwPDB validaton report
Full document	3gr0_full_validation.pdf.gz	456.5 KB	Display
Data in XML	3gr0_validation.xml.gz	29.2 KB	Display
Data in CIF	3gr0_validation.cif.gz	41.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gr/3gr0 ftp://data.pdbj.org/pub/pdb/validation_reports/gr/3gr0	HTTPS FTP

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Related structure data

Related structure data	3gr1C 3gr5C C: citing same article (ref.)
Similar structure data	2a38-2 4g1i-1 2pe6-d 3rcz-d 2a38-3 5knh-d 6oq2-d 3tg8-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

Related structure data

3gr1C

3gr5C

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Protein prgH

B: Protein prgH

C: Protein prgH

D: Protein prgH

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

1

A: Protein prgH

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

2

B: Protein prgH

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

3

C: Protein prgH

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

4

D: Protein prgH

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

Unit cell

Length a, b, c (Å)	53.257, 53.257, 282.527
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	144
Space group name H-M	P3₁

#1: Protein	Protein prgH Mass: 22953.041 Da / Num. of mol.: 4 / Fragment: PrgH periplasmic domain, residues 170-362 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: prgH, STM2874 / Production host: Escherichia coli (E. coli) / References: UniProt: P41783
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.52 Å³/Da / Density % sol: 51.18 %
Crystal grow	Method: vapor diffusion, hanging drop / pH: 8.5 Details: 30% (w/v) PEG 1500 + 0.1M lithium sulfate + 0.1M Tris 8.5 + 0.109M octanoyl-n-hydroxyethylglucamide, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2
Detector	Type: ADSC QUANTUM 315 / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Relative weight: 1
Reflection	Resolution: 2.3→35 Å / Num. obs: 39588 / % possible obs: 99.52 %

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
PDB_EXTRACT	3.006	data extraction
MOSFLM		data reduction
SCALA		data scaling
SHARP		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.3→35 Å / Cor.coef. F_o:F_c: 0.939 / Cor.coef. F_o:F_c free: 0.911 / Occupancy max: 1 / Occupancy min: 1 / SU B: 12.97 / SU ML: 0.167 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.345 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.255	2006	5.1 %	RANDOM
R_work	0.206	-	-	-
obs	0.208	39588	99.52 %	-

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 max: 64.61 Å² / B_iso mean: 23.526 Å² / B_iso min: 3.5 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.24 Å²	0.62 Å²	0 Å²
2-	-	1.24 Å²	0 Å²
3-	-	-	-1.86 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→35 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6080	0	0	231	6311

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.022	6207
X-RAY DIFFRACTION	r_angle_refined_deg	1.328	1.95	8384
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.58	5	729
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.269	23.027	337
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.45	15	1109
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.375	15	72
X-RAY DIFFRACTION	r_chiral_restr	0.086	0.2	881
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	4808
X-RAY DIFFRACTION	r_nbd_refined	0.197	0.2	2427
X-RAY DIFFRACTION	r_nbtor_refined	0.303	0.2	4113
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.151	0.2	311
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.231	0.2	76
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.167	0.2	19
X-RAY DIFFRACTION	r_mcbond_it	0.761	1.5	3777
X-RAY DIFFRACTION	r_mcangle_it	1.242	2	5875
X-RAY DIFFRACTION	r_scbond_it	1.99	3	2824
X-RAY DIFFRACTION	r_scangle_it	3.169	4.5	2509

LS refinement shell

Resolution: 2.3→2.36 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.316	145	-
R_work	0.219	2659	-
all	-	2804	-
obs	-	-	96.96 %

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	87.8113	-5.3149	-24.1141	11.4006	16.3726	26.6962	-0.5347	2.3162	0.4485	-0.505	0.4919	-0.2342	0.7447	-2.7111	0.0428	0.017	0.0426	0.0718	0.1902	0.3075	0.0415	-8.0968	19.6478	58.8288
2	5.23	-1.1887	0.2667	4.1557	0.1953	1.6615	-0.0202	-0.1952	0.5599	0.3223	0.0292	-0.0171	-0.206	-0.2729	-0.009	0.0967	-0.0322	0.0141	0.05	0.001	0.1278	9.3243	17.8482	58.8018
3	0.865	0.3351	0.4698	1.3556	0.416	4.6098	0.0532	0.0006	-0.0504	-0.0017	-0.0851	0.0071	0.1189	-0.3373	0.0318	0.0384	-0.0121	0.0133	0.0686	0.0087	0.1019	10.8415	3.5241	43.3801
4	2.3717	1.371	-0.2211	3.8803	-0.8533	7.2763	0.0196	-0.0073	0.3234	-0.1099	-0.0842	0.2511	-0.502	-0.3843	0.0645	0.0788	0.0494	0.0375	0.0935	-0.022	0.0565	9.7659	10.655	34.6182
5	10.0841	-2.3261	4.8843	5.5914	-1.6715	9.6376	0.3706	0.9236	-0.6108	-0.5282	-0.0028	-0.4555	1.0673	0.8071	-0.3678	0.1298	0.0454	0.0576	0.0647	-0.1231	0.1065	41.3874	23.1515	38.0191
6	10.9726	-2.8083	-1.3927	5.1839	0.0432	1.7784	-0.0585	0.4378	0.4662	-0.0009	0.0021	-0.5879	0.0491	0.2043	0.0564	0.1394	-0.0407	-0.0332	0.0991	-0.0039	0.1948	37.4386	34.2849	44.8111
7	1.0258	0.4048	-0.0074	1.1409	-0.7382	4.7827	-0.1148	0.0029	0.0068	-0.108	0.0666	0.1354	0.332	-0.1897	0.0482	0.051	-0.0052	-0.0108	0.0049	-0.0146	0.0812	21.9475	26.5113	55.1038
8	2.3903	0.9237	-0.633	2.6019	0.0369	4.3889	-0.0305	-0.2862	-0.1128	0.1996	-0.1365	-0.3841	0.0984	0.8798	0.167	0.0384	0.0426	0.0141	0.1746	0.0177	0.0574	33.1021	28.2733	70.3313
9	6.1845	-4.8909	-4.8016	19.1624	7.3351	11.0147	0.4336	0.5931	0.4353	0.0673	-0.1073	-0.3694	-0.6316	0.4449	-0.3263	-0.0842	-0.0771	0.0405	0.2676	0.0476	-0.0394	20.2598	17.0824	-10.7995
10	2.9811	0.1657	0.6235	8.2599	-3.2607	5.2792	0.0733	0.3949	0.1546	-0.1081	0.1998	0.6678	-0.4398	0.0074	-0.2731	0.017	-0.038	0.0192	0.2804	-0.0343	0.1734	14.2242	13.3628	-3.0076
11	2.0312	0.0503	0.581	1.4409	0.5478	5.8334	-0.0087	0.24	-0.2007	0.0431	0.0732	-0.0797	-0.0872	0.612	-0.0645	-0.0523	-0.011	0.0222	0.1612	-0.0591	0.0878	27.4715	8.1088	10.6175
12	4.8809	-0.7616	-2.0102	3.5046	1.0318	5.1737	-0.0009	0.1226	0.397	0.0699	0.0695	0.1322	-0.7522	0.0814	-0.0686	0.1334	-0.0038	-0.0211	0.0788	0.006	0.0098	21.2672	17.92	19.6628
13	6.7238	3.8787	1.9058	13.509	6.0375	6.3951	0.1017	-0.616	-0.587	-0.1732	-0.1187	0.1678	0.4761	0.3466	0.0169	0.013	0.1255	-0.0208	0.1846	0.0929	0.0334	-8.5291	-4.175	16.1077
14	3.8227	-0.1033	-2.217	2.4806	-1.0928	5.3476	-0.0075	-0.5981	0.225	0.1231	0.199	0.1085	0.0647	0.3502	-0.1915	0.012	0.0268	-0.0545	0.2917	-0.1151	0.0999	-5.195	7.6142	7.7972
15	1.9587	0.2328	-0.5671	0.7121	0.8735	5.834	-0.1236	-0.1744	0.1316	-0.0723	0.0709	-0.0768	0.0452	0.7708	0.0526	-0.0378	0.0421	-0.0308	0.1043	-0.0367	0.0809	0.6762	6.1156	-5.5877
16	3.3855	0.8176	1.8134	4.3125	0.4996	6.6288	-0.0176	-0.086	-0.3213	-0.3384	0.1191	0.1748	0.998	-0.1326	-0.1015	0.1822	-0.0243	0.01	0.1126	0.0047	0.0137	-5.8066	-3.5551	-13.7629

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	177 - 183
2	X-RAY DIFFRACTION	2	A	184 - 242
3	X-RAY DIFFRACTION	3	A	243 - 338
4	X-RAY DIFFRACTION	4	A	339 - 362
5	X-RAY DIFFRACTION	5	B	171 - 199
6	X-RAY DIFFRACTION	6	B	200 - 242
7	X-RAY DIFFRACTION	7	B	243 - 323
8	X-RAY DIFFRACTION	8	B	324 - 362
9	X-RAY DIFFRACTION	9	C	183 - 200
10	X-RAY DIFFRACTION	10	C	201 - 241
11	X-RAY DIFFRACTION	11	C	242 - 333
12	X-RAY DIFFRACTION	12	C	334 - 362
13	X-RAY DIFFRACTION	13	D	183 - 207
14	X-RAY DIFFRACTION	14	D	208 - 273
15	X-RAY DIFFRACTION	15	D	274 - 327
16	X-RAY DIFFRACTION	16	D	328 - 362

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