PDB-3ks2: Crystal Structure of Type-III Secretion Chaperone IpgC from Shige...

ID or keywords:

Entry

Database: PDB / ID: 3ks2

Title

Crystal Structure of Type-III Secretion Chaperone IpgC from Shigella flexneri (residues 10-155)

Components

Chaperone protein ipgC

Keywords

CHAPERONE / TPR motif / Virulence

Function / homology

Function and homology information

identical protein binding / cytoplasm
Similarity search - Function

Biological species

Shigella flexneri (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.3 Å

Authors

Geisbrecht, B.V. / Barta, M.L.

Citation

Journal: Bmc Struct.Biol. / Year: 2010
Title: Evidence for alternative quaternary structure in a bacterial Type III secretion system chaperone
Authors: Barta, M.L. / Zhang, L. / Picking, W.L. / Geisbrecht, B.V.

History

Deposition	Nov 20, 2009	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Aug 25, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 1, 2023	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 / struct_ncs_dom_lim / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3ks2.cif.gz	992.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3ks2.ent.gz	841.9 KB	Display	PDB format
PDBx/mmJSON format	3ks2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3ks2_validation.pdf.gz	600.8 KB	Display	wwPDB validaton report
Full document	3ks2_full_validation.pdf.gz	716.1 KB	Display
Data in XML	3ks2_validation.xml.gz	95.3 KB	Display
Data in CIF	3ks2_validation.cif.gz	124.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ks/3ks2 ftp://data.pdbj.org/pub/pdb/validation_reports/ks/3ks2	HTTPS FTP

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Related structure data

Related structure data	3gyzS S: Starting model for refinement
Similar structure data	6akg-1 7a26-5 6akg-2 6akf-1 2r51-d 5mk2-1 6h4k-d 3aqj-1 7a27-1 6hem-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) 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

3gyzS

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#32 - Aug 2002 Chaperones similarity (1)

Deposited unit

A: Chaperone protein ipgC

B: Chaperone protein ipgC

C: Chaperone protein ipgC

D: Chaperone protein ipgC

E: Chaperone protein ipgC

F: Chaperone protein ipgC

G: Chaperone protein ipgC

H: Chaperone protein ipgC

I: Chaperone protein ipgC

J: Chaperone protein ipgC

K: Chaperone protein ipgC

L: Chaperone protein ipgC

M: Chaperone protein ipgC

N: Chaperone protein ipgC

O: Chaperone protein ipgC

P: Chaperone protein ipgC

Q: Chaperone protein ipgC

R: Chaperone protein ipgC

308 kDa, 18 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Chaperone protein ipgC

B: Chaperone protein ipgC

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

2

C: Chaperone protein ipgC

D: Chaperone protein ipgC

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

3

E: Chaperone protein ipgC

F: Chaperone protein ipgC

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

4

G: Chaperone protein ipgC

H: Chaperone protein ipgC

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

5

I: Chaperone protein ipgC

J: Chaperone protein ipgC

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

6

K: Chaperone protein ipgC

L: Chaperone protein ipgC

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

7

M: Chaperone protein ipgC

N: Chaperone protein ipgC

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

8

O: Chaperone protein ipgC

P: Chaperone protein ipgC

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

9

Q: Chaperone protein ipgC

R: Chaperone protein ipgC

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

Unit cell

Length a, b, c (Å)	140.496, 71.474, 171.012
Angle α, β, γ (deg.)	90.00, 93.86, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 18 - 154 / Label seq-ID: 14 - 150

Dom-ID	Selection details	Auth asym-ID	Label asym-ID
1	chain A and (resseq 18:154 )	A	A
2	chain B and (resseq 18:154 )	B	B
3	chain C and (resseq 18:154 )	C	C
4	chain D and (resseq 18:154 )	D	D
5	chain E and (resseq 18:154 )	E	E
6	chain F and (resseq 18:154 )	F	F
7	chain G and (resseq 18:154 )	G	G
8	chain H and (resseq 18:154 )	H	H
9	chain I and (resseq 18:154 )	I	I
10	chain J and (resseq 18:154 )	J	J
11	chain K and (resseq 18:154 )	K	K
12	chain L and (resseq 18:154 )	L	L
13	chain M and (resseq 18:154 )	M	M
14	chain N and (resseq 18:154 )	N	N
15	chain O and (resseq 18:154 )	O	O
16	chain P and (resseq 18:154 )	P	P
17	chain Q and (resseq 18:154 )	Q	Q
18	chain R and (resseq 18:154 )	R	R

#1: Protein	Chaperone protein ipgC Mass: 17129.346 Da / Num. of mol.: 18 / Fragment: residues 10-155 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: ipgC / Plasmid: pT7HMT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A2U4

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.78 Å³/Da / Density % sol: 55.73 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2M magnesium chloride hexahydrate, 0.1M HEPES, 25% PEG 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 12, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3.3→50 Å / Num. obs: 45608 / B_iso Wilson estimate: 68.53 Å²

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASER		phasing
PHENIX	(phenix.refine)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3gyz

3gyz

Resolution: 3.3→46.726 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.757 / SU ML: 0.52 / σ(F): 1.33 / Phase error: 30.83 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2962	1983	4.35 %	RANDOM
R_work	0.2588	-	-	-
obs	0.2605	45608	88 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 51.665 Å² / k_sol: 0.315 e/Å³

Displacement parameters

B_iso max: 208.27 Å² / B_iso mean: 98.227 Å² / B_iso min: 28.61 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-29.927 Å²	0 Å²	9.326 Å²
2-	-	32.075 Å²	-0 Å²
3-	-	-	-2.148 Å²

Refinement step

Cycle: LAST / Resolution: 3.3→46.726 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20052	0	0	0	20052

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	20502
X-RAY DIFFRACTION	f_angle_d	1.285	27684
X-RAY DIFFRACTION	f_chiral_restr	0.099	2952
X-RAY DIFFRACTION	f_plane_restr	0.004	3600
X-RAY DIFFRACTION	f_dihedral_angle_d	19.668	7326

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	1115	X-RAY DIFFRACTION	POSITIONAL	0.084
1	2	B	1115	X-RAY DIFFRACTION	POSITIONAL	0.084
1	3	C	1115	X-RAY DIFFRACTION	POSITIONAL	0.059
1	4	D	1115	X-RAY DIFFRACTION	POSITIONAL	0.07
1	5	E	1115	X-RAY DIFFRACTION	POSITIONAL	0.059
1	6	F	1115	X-RAY DIFFRACTION	POSITIONAL	0.07
1	7	G	1115	X-RAY DIFFRACTION	POSITIONAL	0.065
1	8	H	1115	X-RAY DIFFRACTION	POSITIONAL	0.077
1	9	I	1115	X-RAY DIFFRACTION	POSITIONAL	0.059
1	10	J	1115	X-RAY DIFFRACTION	POSITIONAL	0.078
1	11	K	1115	X-RAY DIFFRACTION	POSITIONAL	0.058
1	12	L	1115	X-RAY DIFFRACTION	POSITIONAL	0.058
1	13	M	1115	X-RAY DIFFRACTION	POSITIONAL	0.058
1	14	N	1115	X-RAY DIFFRACTION	POSITIONAL	0.066
1	15	O	1115	X-RAY DIFFRACTION	POSITIONAL	0.068
1	16	P	1115	X-RAY DIFFRACTION	POSITIONAL	0.07
1	17	Q	1115	X-RAY DIFFRACTION	POSITIONAL	0.076
1	18	R	1115	X-RAY DIFFRACTION	POSITIONAL	0.074

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
3.3-3.382	0.372	75	0.339	1652	1727	24
3.382-3.474	0.361	89	0.31	1932	2021	28
3.474-3.576	0.32	101	0.292	2263	2364	33
3.576-3.691	0.323	126	0.285	2717	2843	40
3.691-3.823	0.35	152	0.296	3261	3413	48
3.823-3.976	0.313	142	0.289	3491	3633	51
3.976-4.157	0.326	174	0.275	3487	3661	51
4.157-4.376	0.277	158	0.233	3499	3657	51
4.376-4.65	0.277	159	0.237	3525	3684	52
4.65-5.009	0.261	164	0.23	3511	3675	52
5.009-5.512	0.32	159	0.244	3533	3692	52
5.512-6.308	0.279	162	0.261	3561	3723	52
6.308-7.941	0.235	160	0.208	3577	3737	52
7.941-46.73	0.244	162	0.226	3616	3778	53

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	1.2934	-0.0833	-0.11	-0.0938	0.1588	0.5213	0.01	0.2084	-0.0507	-0.1046	0.0418	-0.098	-0.1454	-0.1622	-0	0.4468	-0.0463	-0.0477	0.2535	0.0364	0.395	19.0023	-8.4093	-6.9884
2	-0.0331	-0.9038	-1.6639	-1.1773	-0.2965	1.827	0.0568	0.1564	0.0255	0.1274	-0.0832	-0.1569	0.0072	0.3536	-0	0.4877	-0.0014	0.0417	0.3379	0.0481	0.5947	50.5314	-4.3552	-17.6467
3	0.8662	-0.3196	0.4552	-0.2293	0.0524	-0.2881	0.1894	0.2525	0.0432	0.1221	-0.0063	-0.1108	-0.1197	0.0954	-0	0.4862	0.1318	-0.0449	0.5763	0.1296	0.4347	18.5941	27.7456	17.523
4	0.1382	-0.5188	-2.5046	-0.0815	0.0461	0.9642	0.0628	-0.4305	-0.0842	0.0781	-0.1088	-0.1761	-0.0682	0.3373	0	0.5303	0.0075	-0.03	0.8281	0.1131	0.4374	50.6735	27.9251	7.6707
5	2.842	-0.4891	-0.2902	-0.0801	-0.0033	-0.4882	-0.1189	0.0329	-0.1536	0.0709	0.0434	-0.1433	-0.2886	-0.5151	-0	0.543	0.0604	-0.0735	0.5187	0.0368	0.3318	32.2105	1.5941	31.7439
6	1.2713	-0.0917	-0.8756	0.2755	0.2307	0.4172	0.0783	0.454	-0.107	0.0618	-0.0033	-0.0466	-0.011	-0.1208	-0	0.5367	0.0019	-0.0352	0.3007	-0.0443	0.4273	64.2993	-1.5605	21.8197
7	1.2348	-0.4339	-1.6638	-0.6808	0.2131	0.3076	-0.1073	0.2631	-0.548	-0.0105	-0.2076	-0.057	-0.2024	-0.0818	-0	0.462	0.0295	-0.0148	0.176	-0.0004	0.4237	38.4971	32.4491	-31.0227
8	0.9284	-0.3896	-1.5065	-0.2777	0.1087	0.5014	0.218	0.3487	-0.1334	0.0867	-0.1196	-0.0072	0.0165	0.0386	-0	0.4115	0.0464	-0.0439	0.4564	-0.005	0.474	5.7888	30.7536	-22.4737
9	1.3538	0.0295	1.585	-1.4484	-0.1822	1.8458	0.3988	0.2166	-0.2029	0.0578	-0.0025	0.0323	-0.037	-0.4003	-0	0.5616	0.0375	0.1155	0.1821	-0.0748	0.7173	64.9006	45.0809	44.9008
10	1.3505	-1.708	-0.8319	0.3532	0.6449	-1.5727	0.177	-0.1241	0.0318	-0.2559	-0.2005	-0.2392	-0.0936	-0.0742	0	0.5806	0.0836	-0.0399	1.0307	0.1297	0.4087	32.1057	48.7838	52.3873
11	1.9461	0.0361	-1.2667	0.7073	-0.3446	0.1524	-0.2316	-0.1674	-0.6787	-0.1314	-0.2113	-0.0261	0.2268	0.0539	0	0.6211	0.0317	0.1365	0.3288	0.1438	0.6702	37.6273	7.2339	-54.6233
12	1.557	0.6112	-1.095	-0.2434	0.2041	-0.0956	0.047	0.4379	-0.212	-0.0508	-0.0653	-0.0368	0.0982	-0.0593	0	0.5931	-0.0523	0.0491	0.6588	-0.0011	0.5588	5.5004	2.6422	-45.8658
13	0.2978	-0.7683	-1.8318	0.0067	0.2835	1.6372	-0.042	-0.1156	0.0725	0.0923	0.1353	-0.1776	0.1158	-0.1894	0	0.6002	-0.0863	0.0839	0.5145	-0.186	0.5529	77.7461	-8.6109	76.2633
14	1.1804	0.1845	-0.9343	1.0174	-0.5276	-0.5174	-0.2745	0.5701	0.3389	-0.0978	0.6851	0.6563	-0.0825	-0.1816	0	0.6404	-0.0515	0.0036	1.009	0.3236	0.7085	46.15	-8.581	87.2203
15	-0.135	-1.654	-0.1437	-0.1992	0.0616	0.3269	-0.2841	-0.757	0.2679	0.2768	0.1376	-0.0521	0.0493	0.0449	-0	0.6953	-0.0955	0.0855	1.0588	-0.3634	0.8801	-26.0285	4.2074	78.7788
16	0.357	-0.7018	-0.2452	0.5595	-0.5833	0.1656	0.3805	-0.7041	0.4181	0.1592	-0.5253	-0.0036	-0.1407	0.4034	0	0.596	-0.1134	-0.0313	0.9666	-0.0422	0.6675	6.0188	0.5151	69.2638
17	0.8043	-1.5433	-1.6905	1.3481	1.1831	2.0495	0.2782	-0.9298	-0.5609	0.0223	-0.0519	0.3584	0.0177	-0.3091	-0	0.5806	-0.0907	-0.0561	0.4625	-0.0471	0.5791	73.8735	15.0505	52.2471
18	0.9417	2.2157	0.5986	-1.0274	0.042	0.0685	0.4614	-0.2721	-0.3652	0.005	-0.2149	-0.2916	0.1336	-0.1054	-0	0.7351	-0.0899	-0.1235	0.9573	0.1923	1.4346	40.9405	17.9437	62.5524

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain A	A	18 - 154
2	X-RAY DIFFRACTION	2	chain B	B	18 - 154
3	X-RAY DIFFRACTION	3	chain C	C	18 - 154
4	X-RAY DIFFRACTION	4	chain D	D	18 - 154
5	X-RAY DIFFRACTION	5	chain E	E	18 - 154
6	X-RAY DIFFRACTION	6	chain F	F	18 - 154
7	X-RAY DIFFRACTION	7	chain G	G	18 - 154
8	X-RAY DIFFRACTION	8	chain H	H	18 - 154
9	X-RAY DIFFRACTION	9	chain I	I	18 - 154
10	X-RAY DIFFRACTION	10	chain J	J	18 - 154
11	X-RAY DIFFRACTION	11	chain K	K	18
12	X-RAY DIFFRACTION	12	chain L	L	18 - 154
13	X-RAY DIFFRACTION	13	chain M	M	18 - 154
14	X-RAY DIFFRACTION	14	chain N	N	18 - 154
15	X-RAY DIFFRACTION	15	chain O	O	18 - 154
16	X-RAY DIFFRACTION	16	chain P	P	18 - 154
17	X-RAY DIFFRACTION	17	chain Q	Q	18 - 154
18	X-RAY DIFFRACTION	18	chain R	R	18 - 154

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