PDB-3blc: Crystal structure of the periplasmic domain of the Escherichia Co...

ID or keywords:

Entry

Database: PDB / ID: 3blc

Title

Crystal structure of the periplasmic domain of the Escherichia Coli YIDC

Components

Inner membrane protein oxaA

Keywords

CHAPERONE / PROTEIN TRANSPORT / YidC / membrane assembly facilitator / periplasmic domain / Inner membrane / Transmembrane / OXAA

Function / homology

Function and homology information

protein localization to chloroplast / protein insertion into membrane from inner side / membrane insertase activity / thylakoid membrane organization / cell envelope Sec protein transport complex / protein transport by the Sec complex / protein insertion into membrane / protein folding / protein-containing complex assembly / membrane / plasma membrane
Similarity search - Function

Biological species

Escherichia coli K12 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.5 Å

Authors

Paetzel, M. / Oliver, D.C.

Citation

Journal: J.Biol.Chem. / Year: 2008
Title: Crystal Structure of the Major Periplasmic Domain of the Bacterial Membrane Protein Assembly Facilitator YidC.
Authors: Oliver, D.C. / Paetzel, M.

History

Deposition	Dec 10, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 25, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Oct 20, 2021	Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3blc.cif.gz	117.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3blc.ent.gz	98.6 KB	Display	PDB format
PDBx/mmJSON format	3blc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3blc_validation.pdf.gz	444.2 KB	Display	wwPDB validaton report
Full document	3blc_full_validation.pdf.gz	455.5 KB	Display
Data in XML	3blc_validation.xml.gz	21.9 KB	Display
Data in CIF	3blc_validation.cif.gz	30.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bl/3blc ftp://data.pdbj.org/pub/pdb/validation_reports/bl/3blc	HTTPS FTP

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Related structure data

Similar structure data	6hdv-2 6hdv-3 2yt0-d 4obm-d 2vfx-8 3elf-d 2vfx-5 5a7i-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) 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	#32 - Aug 2002 Chaperones similarity (1)

Deposited unit

A: Inner membrane protein oxaA

B: Inner membrane protein oxaA

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

1

A: Inner membrane protein oxaA

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

2

B: Inner membrane protein oxaA

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

3

A: Inner membrane protein oxaA

B: Inner membrane protein oxaA

A: Inner membrane protein oxaA

B: Inner membrane protein oxaA

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

Unit cell

Length a, b, c (Å)	126.127, 126.127, 288.459
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	98
Space group name H-M	I4₁22

#1: Protein	Inner membrane protein oxaA Mass: 35963.898 Da / Num. of mol.: 2 / Fragment: UNP residues 26-340 / Mutation: E228A, K229A, E231A, K232A, K234A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: oxaA, yidC / Plasmid: pET20b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P25714
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Inner membrane protein oxaA

Mass: 35963.898 Da / Num. of mol.: 2 / Fragment: UNP residues 26-340 / Mutation: E228A, K229A, E231A, K232A, K234A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: oxaA, yidC / Plasmid: pET20b / Species (production host): Escherichia coli / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P25714

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 80 / 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: 3.99 Å³/Da / Density % sol: 69.15 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 3.1 Details: 0.1 M glycine, 0.2 M ammonium sulfate, 13% PEG3350, pH 3.1, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9794 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 2, 2007 / Details: mirrors
Radiation	Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 2.5→50 Å / Num. obs: 40327 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13.8 % / R_merge(I) obs: 0.079 / R_sym value: 0.079 / Net I/σ(I): 44.7
Reflection shell	Resolution: 2.5→2.6 Å / Redundancy: 9.7 % / R_merge(I) obs: 0.379 / Mean I/σ(I) obs: 4 / Num. unique all: 3687 / R_sym value: 0.379 / % possible all: 92

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
ADSC	Quantum	data collection
HKL-2000		data reduction
HKL-2000		data scaling
SHELXS		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.5→50 Å / Cor.coef. F_o:F_c: 0.94 / Cor.coef. F_o:F_c free: 0.911 / SU B: 13.891 / SU ML: 0.151 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.248 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24897	2021	5 %	RANDOM
R_work	0.21165	-	-	-
obs	0.2135	38278	98.93 %	-

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: 34.447 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.13 Å²	0 Å²	0 Å²
2-	-	2.13 Å²	0 Å²
3-	-	-	-4.26 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4291	0	0	80	4371

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	4401
X-RAY DIFFRACTION	r_angle_refined_deg	1.515	1.953	6020
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.994	5	554
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.488	25.764	203
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.498	15	654
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.166	15	11
X-RAY DIFFRACTION	r_chiral_restr	0.103	0.2	664
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	3443
X-RAY DIFFRACTION	r_nbd_refined	0.223	0.2	1689
X-RAY DIFFRACTION	r_nbtor_refined	0.315	0.2	2919
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.142	0.2	175
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.227	0.2	60
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.174	0.2	8
X-RAY DIFFRACTION	r_mcbond_it	0.665	1.5	2841
X-RAY DIFFRACTION	r_mcangle_it	1.018	2	4472
X-RAY DIFFRACTION	r_scbond_it	1.819	3	1810
X-RAY DIFFRACTION	r_scangle_it	2.62	4.5	1548

LS refinement shell

Resolution: 2.5→2.563 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.311	134	-
R_work	0.294	2497	-
obs	-	-	88.56 %

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	5.7191	-2.0615	2.399	1.6002	-2.3787	9.6655	0.2858	0.7492	-0.178	-0.705	-0.3479	0.1126	1.1987	-0.3445	0.0621	0.6075	-0.2735	-0.0676	0.3094	-0.0367	0.0733	71.6229	39.7348	109.0839
2	1.462	-0.0956	-2.719	3.5009	-2.4498	11.0971	-0.1346	0.208	-0.1688	-0.3878	-0.0312	-0.1114	1.086	0.5218	0.1657	0.3455	-0.1682	0.0285	0.0974	0.011	-0.0143	82.4099	39.2771	118.6429
3	0.758	0.1308	1.3918	3.1496	0.2786	4.8001	-0.0214	0.2113	-0.2173	-0.2178	0.1395	0.2403	1.0646	-0.4777	-0.1181	0.7002	-0.3752	-0.0415	0.3895	0.0484	0.1498	69.7797	33.1063	125.0179
4	1.8099	0.2625	-0.4255	1.672	-0.0787	4.4848	0.0761	-0.2209	-0.2469	-0.0114	-0.0243	0.3462	0.7467	-0.5832	-0.0518	0.2664	-0.2283	0.0285	0.0967	-0.0096	0.0065	75.3224	41.4402	125.8398
5	6.2586	-3.6031	-2.7255	9.1175	0.7624	1.2793	0.2384	0.8395	-0.4324	-1.5811	-0.4007	0.2296	-0.7738	-1.2131	0.1623	0.1918	-0.1105	0.0888	0.1418	0.0199	0.0131	85.3236	53.4979	110.2363
6	5.0929	-3.0241	-1.9338	3.249	-0.0189	4.8025	0.1589	-0.0445	0.0829	-0.0874	-0.1077	-0.1395	0.5433	-0.0869	-0.0511	0.1205	-0.0817	0.1012	-0.0693	0.0186	-0.1114	88.9358	55.6644	120.6851
7	3.4075	0.1936	-0.6624	2.4771	-0.917	5.3498	0.239	0.0676	0.0441	-0.2551	-0.1296	0.1575	0.1913	-0.1988	-0.1094	0.1878	-0.1456	0.0359	-0.0968	-0.0222	-0.125	83.0844	50.0516	119.8052
8	0.5455	1.5712	-2.3818	4.528	-7.0188	20.5083	0.2071	0.2588	0.0993	-0.335	0.2721	0.2817	0.5254	-0.2485	-0.4793	0.146	-0.1228	-0.0145	0.1045	0.0773	-0.0542	79.7543	43.7326	138.4469
9	2.3313	2.4782	-3.9473	3.0468	-6.3717	18.1605	0.5665	-0.3397	-0.4084	0.3227	0.1736	0.2636	0.0122	0.2445	-0.7401	0.4011	-0.2342	0.0574	0.2802	-0.0127	0.0539	72.2024	45.7354	128.0671
10	11.4365	2.7236	-11.9164	4.2107	4.2737	26.6144	1.1243	-0.8052	1.7016	0.7983	-0.1048	0.9481	-1.6223	0.3312	-1.0194	0.5578	-0.1383	0.1865	0.4511	-0.0321	0.3959	71.6179	59.1838	116.9065
11	9.9502	1.0332	-8.0836	1.6835	0.6711	9.933	0.1853	0.8198	0.413	-0.0268	0.0717	0.091	-0.0368	-0.9181	-0.2569	0.0123	0.0421	0.0713	-0.0089	0.0541	-0.0292	90.9651	64.146	104.0225
12	7.3976	1.571	-0.2149	0.8137	1.1239	2.8556	-0.1974	0.2796	-0.2165	-0.602	0.8894	1.0672	0.1264	-1.5077	-0.6921	0.2707	-0.2167	0.0702	0.785	0.0158	0.2292	71.9835	70.4366	79.4987
13	6.8925	1.0253	0.8902	8.8408	-4.9784	9.6088	-0.1117	0.0144	-0.7017	0.4259	1.0123	1.0384	0.2312	-1.9231	-0.9006	0.0852	-0.0578	0.0906	0.5131	0.115	0.2475	72.5087	69.0321	89.9758
14	2.27	3.6367	-5.3401	6.6713	-6.952	15.604	0.4928	0.9313	0.866	0.5611	0.6399	0.8031	-1.0066	-1.4233	-1.1326	0.0828	0.1573	0.1353	0.4465	0.2686	0.2487	76.0197	84.3723	84.7152
15	4.5559	-0.003	1.3448	7.7014	-1.7172	4.6996	-0.0246	0.9169	-0.1027	-0.9523	0.2014	0.3229	0.3832	-0.8849	-0.1768	0.2389	-0.1433	0.1054	0.9295	0.0658	0.1574	76.2216	73.7244	74.2076
16	4.7319	-12.8729	5.3186	36.2001	-15.825	7.6239	-0.2779	1.0199	0.361	-0.8402	0.4497	-0.4139	0.5703	-1.2383	-0.1718	0.2912	-0.2058	0.0116	1.0421	0.1141	0.1705	78.8233	76.5694	70.1741
17	2.5585	1.5275	-1.9258	1.9017	-2.2167	5.0828	-0.1289	0.9949	0.1492	-0.6415	0.362	0.0862	0.0424	-0.694	-0.2331	0.1441	-0.0406	0.0803	0.4771	0.1084	0.1031	84.429	80.3726	74.9682
18	39.1464	-3.3512	9.94	0.9341	0.6741	6.1172	0.9539	-3.2547	-3.1744	0.7088	0.1902	0.4666	0.3241	-1.9787	-1.1441	0.4565	0.0228	0.2066	0.7281	0.3288	0.5445	72.7084	78.1827	102.8511
19	10.141	-3.0679	-3.7338	6.0993	-0.6009	8.0219	0.3549	-0.2126	1.0063	0.2247	0.0663	0.2269	-0.9711	-0.2266	-0.4212	0.2373	0.0395	0.1589	0.0183	0.0185	0.0388	87.902	87.6388	98.9502
20	0.8359	0.4047	0.4646	5.7542	-1.2433	2.7611	0.1577	0.3026	0.1895	0.198	0.0907	0.3839	-0.5285	-0.3936	-0.2485	0.0463	0.0394	0.118	0.0982	0.0814	-0.0318	85.9911	82.3913	91.8269
21	3.0315	1.5512	-1.9198	2.5252	-4.84	9.8109	0.1423	0.668	0.1147	-0.1768	0.2203	0.1919	0.1307	-0.1193	-0.3626	0.2393	0.0267	0.1265	0.3185	0.153	0.1006	91.3941	88.3578	73.3765
22	1.7967	0.3722	0.5863	1.7328	0.0651	7.4961	0.0207	0.1377	-0.002	0.1754	0.1143	0.0732	0.3383	-0.658	-0.1349	0.007	0.0205	0.1228	0.0291	0.0234	0.0855	88.7556	72.2833	100.4115

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	57 - 98	33 - 74
2	X-RAY DIFFRACTION	2	A	A	99 - 121	75 - 97
3	X-RAY DIFFRACTION	3	A	A	122 - 160	98 - 136
4	X-RAY DIFFRACTION	4	A	A	161 - 203	137 - 179
5	X-RAY DIFFRACTION	5	A	A	204 - 226	180 - 202
6	X-RAY DIFFRACTION	6	A	A	227 - 255	203 - 231
7	X-RAY DIFFRACTION	7	A	A	256 - 287	232 - 263
8	X-RAY DIFFRACTION	8	A	A	288 - 298	264 - 274
9	X-RAY DIFFRACTION	9	A	A	299 - 309	275 - 285
10	X-RAY DIFFRACTION	10	A	A	310 - 324	286 - 300
11	X-RAY DIFFRACTION	11	A	A	325 - 346	301 - 322
12	X-RAY DIFFRACTION	12	B	B	56 - 67	32 - 43
13	X-RAY DIFFRACTION	13	B	B	68 - 101	44 - 77
14	X-RAY DIFFRACTION	14	B	B	102 - 121	78 - 97
15	X-RAY DIFFRACTION	15	B	B	122 - 146	98 - 122
16	X-RAY DIFFRACTION	16	B	B	147 - 155	123 - 131
17	X-RAY DIFFRACTION	17	B	B	156 - 197	132 - 173
18	X-RAY DIFFRACTION	18	B	B	198 - 220	174 - 196
19	X-RAY DIFFRACTION	19	B	B	221 - 246	197 - 222
20	X-RAY DIFFRACTION	20	B	B	247 - 286	223 - 262
21	X-RAY DIFFRACTION	21	B	B	287 - 301	263 - 277
22	X-RAY DIFFRACTION	22	B	B	302 - 343	278 - 319

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