PDB-2yms: Structure and assembly of a b-propeller with nine blades and a ne...

ID or keywords:

Entry

Database: PDB / ID: 2yms

Title

Structure and assembly of a b-propeller with nine blades and a new conserved repetitive sequence motif

Components

(OUTER MEMBRANE PROTEIN ASSEMBLY FACTOR ...) x 4

Keywords

CHAPERONE / PROPELLER STRUCTURE / ASSEMBLED FROM FRAGMENTS / NINE BLADES

Function / homology

Function and homology information

Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / cell outer membrane /

membrane / identical protein binding
Similarity search - Function

Biological species

ESCHERICHIA COLI (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.101 Å

Authors

Zeth, K. / Albrecht, R.

Citation

Journal: To be Published
Title: Structure and Assembly of a B-Propeller with Nine Blades and a New Conserved Repetitive Sequence Motif
Authors: Albrecht, R. / Zeth, K.

History

Deposition	Oct 10, 2012	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 30, 2013	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2yms.cif.gz	142.6 KB	Display	PDBx/mmCIF format
PDB format	pdb2yms.ent.gz	118.9 KB	Display	PDB format
PDBx/mmJSON format	2yms.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ym/2yms ftp://data.pdbj.org/pub/pdb/validation_reports/ym/2yms	HTTPS FTP

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Related structure data

Related structure data	2ymk 2ymu
Similar structure data	3qsu-1 2xf7-d 2xf5-d 6jy5-d 2dsy-d 2xf6-1 4ht8-d 6tjc-d Search similar-shape structures by Omokage search (details) 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
Related items in Molecule of the Month	#32 - Aug 2002 Chaperones similarity (1) #261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #29 - May 2002 Penicillin-binding Proteins similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

Deposited unit

A: OUTER MEMBRANE PROTEIN ASSEMBLY FACTOR BAMB

B: OUTER MEMBRANE PROTEIN ASSEMBLY FACTOR BAMB

C: OUTER MEMBRANE PROTEIN ASSEMBLY FACTOR BAMB

D: OUTER MEMBRANE PROTEIN ASSEMBLY FACTOR BAMB

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	88.570, 83.450, 57.370
Angle α, β, γ (deg.)	90.00, 118.94, 90.00
Int Tables number	5
Space group name H-M	C121

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OUTER MEMBRANE PROTEIN ASSEMBLY FACTOR ... , 4 types, 4 molecules ABCD

#1: Protein	OUTER MEMBRANE PROTEIN ASSEMBLY FACTOR BAMB Mass: 13599.114 Da / Num. of mol.: 1 / Fragment: FRAGMENTS OF BAMB FROM E. COLI, RESIDUES 62-191 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: BL21List of strains of Escherichia coli / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P77774
#2: Protein	OUTER MEMBRANE PROTEIN ASSEMBLY FACTOR BAMB Mass: 7600.385 Da / Num. of mol.: 1 / Fragment: FRAGMENTS OF BAMB FROM E. COLI, RESIDUES 113-186 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: BL21List of strains of Escherichia coli / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P77774
#3: Protein	OUTER MEMBRANE PROTEIN ASSEMBLY FACTOR BAMB Mass: 8261.299 Da / Num. of mol.: 1 / Fragment: FRAGMENTS OF BAMB FROM E. COLI, RESIDUES 248-322 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: BL21List of strains of Escherichia coli / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P77774
#4: Protein	OUTER MEMBRANE PROTEIN ASSEMBLY FACTOR BAMB Mass: 8132.185 Da / Num. of mol.: 1 / Fragment: FRAGMENTS OF BAMB FROM E. COLI, RESIDUES 249-320 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: BL21List of strains of Escherichia coli / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P77774

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Non-polymers , 2 types, 94 molecules

#5: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H₂O

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Details

Sequence details	THE PROTEIN CRYSTAL ASSEMBLED FROM FRAGMENTS OF BAMB OF E. COLI

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.47 Å³/Da / Density % sol: 49.84 % / Description: NONE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
Detector	Type: DECTRIS PILATUS / Detector: PIXEL
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.1→50 Å / Num. obs: 21022 / % possible obs: 93.4 % / Observed criterion σ(I): 1.6 / Redundancy: 2.1 % / R_merge(I) obs: 0.06 / Net I/σ(I): 7.4
Reflection shell	Resolution: 2.1→2.2 Å / Redundancy: 2.1 % / R_merge(I) obs: 0.45 / Mean I/σ(I) obs: 1.6 / % possible all: 91.2

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE: 1.8.1_1168)	refinement
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.101→50.206 Å / SU ML: 0.23 / σ(F): 2.02 / Phase error: 26.71 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2395	1079	5.1 %
R_work	0.187	-	-
obs	0.1899	21018	98.59 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.101→50.206 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2588	0	1	93	2682

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	2635
X-RAY DIFFRACTION	f_angle_d	1.069	3597
X-RAY DIFFRACTION	f_dihedral_angle_d	14.665	907
X-RAY DIFFRACTION	f_chiral_restr	0.076	433
X-RAY DIFFRACTION	f_plane_restr	0.003	462

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 (%)
2.1013-2.197	0.3374	116	0.2626	2378	X-RAY DIFFRACTION	95
2.197-2.3128	0.3069	120	0.2504	2512	X-RAY DIFFRACTION	100
2.3128-2.4577	0.2871	135	0.2439	2497	X-RAY DIFFRACTION	99
2.4577-2.6474	0.3066	129	0.231	2512	X-RAY DIFFRACTION	99
2.6474-2.9138	0.2737	167	0.2043	2481	X-RAY DIFFRACTION	100
2.9138-3.3354	0.2619	137	0.1853	2529	X-RAY DIFFRACTION	100
3.3354-4.2019	0.2218	140	0.1604	2523	X-RAY DIFFRACTION	99
4.2019-50.2203	0.1899	135	0.1615	2507	X-RAY DIFFRACTION	97

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	1.4039	0.522	0.9849	0.5015	0.304	0.6635	-0.1901	0.2351	-0.1785	-0.3472	-0.1674	0.3253	-0.2093	-0.1822	-0.0009	0.4588	-0.0489	-0.0024	0.3111	0.0332	0.4496	6.5527	0.3375	24.2616
2	0.6308	0.5746	0.0667	0.6292	-0.2136	0.5473	-0.1262	-0.1045	0.1666	0.356	0.078	-0.3423	-0.4331	0.2272	0.0002	0.3771	-0.016	-0.0594	0.3151	0.0003	0.4319	11.4397	2.0493	32.0664
3	0.3303	-0.0209	0.1308	0.1288	0.0917	0.837	-1	0.4945	0.4507	-0.8117	0.6058	0.0968	0.181	0.2394	-0.1146	0.4738	-0.019	-0.0547	0.4134	-0.0025	0.6172	15.8681	-7.473	18.28
4	0.9351	0.1703	0.6175	0.7761	0.4439	0.4758	0.0082	-0.1674	0.2641	0.0999	0.0268	-0.0285	-0.1622	0.2459	0.0004	0.4828	-0.0385	-0.0227	0.3374	0.053	0.3603	6.982	-10.7163	23.0421
5	1.917	-0.017	0.1815	1.6408	-0.2638	1.6986	-0.0722	0.1878	0.1245	-0.1224	0.0854	-0.0081	0.0304	-0.0127	0.0002	0.2998	-0.0032	-0.0038	0.2442	0.0317	0.2644	2.8625	-14.0718	19.266
6	1.572	0.6257	-0.3764	0.9711	-0.9431	0.8535	-0.3103	0.4316	0.1243	-0.4623	0.1209	0.2187	-0.3798	-0.2496	-0.0001	0.5191	0.012	-0.0269	0.4739	0.0098	0.4533	-2.7823	-21.0248	13.9601
7	2.1754	-1.3144	-0.0849	0.9371	0.4541	0.6132	0.4006	0.188	-0.5942	-0.4891	-0.4468	-0.1994	0.1431	0.019	0.0006	0.4852	0.1037	0.001	0.5656	0.0006	0.4357	-9.9702	-14.3275	11.8789
8	1.0214	-1.3072	0.4081	2.0287	-0.6744	0.1807	0.543	0.2444	-0.3082	-0.7207	-0.5224	0.1367	-0.0958	0.0707	-0.0021	0.6175	0.1054	-0.0602	0.6128	-0.1227	0.4479	-17.7404	-7.4774	3.3701
9	0.1452	0.2018	0.1544	0.2714	0.2238	0.17	0.3006	0.6534	0.0674	-0.0079	-0.089	-0.0682	0.2762	-0.7766	0.0018	0.4258	0.0606	0.0612	0.6111	-0.1307	0.3478	-18.1788	4.6971	7.5328
10	4.7463	2.6339	-1.7837	1.6806	-0.8443	0.8364	0.6597	0.3959	0.3268	-0.4861	-0.4531	0.9182	-0.6631	0.4141	-0.0475	0.3484	0.1274	-0.0456	0.6815	-0.0939	0.4411	-16.2355	8.2237	-1.0151
11	0.8114	-0.8267	-0.3326	0.824	0.4329	0.3775	0.2522	0.4506	-0.2628	-0.9375	-0.5503	-0.0165	0.1032	0.4473	-0.0028	0.5694	0.09	-0.1051	0.6483	-0.0965	0.3915	-23.7117	7.6804	1.3431
12	1.2872	0.5596	0.6952	3.8162	0.2327	2.005	0.8085	0.1684	-0.5154	-0.9357	-0.9137	-0.8931	2.2824	1.4274	0.4097	0.4316	0.2293	0.1018	1.0225	0.0581	0.1813	-8.5266	9.9367	3.3233
13	0.2727	-0.001	0.1354	0.3914	0.0029	0.054	0.1949	0.9932	0.2898	-0.4679	-0.1861	0.2836	-0.0677	-0.3298	-0.0006	0.3249	-0.0056	0.0496	0.5312	-0.0021	0.2666	-14.0973	12.9707	12.2566
14	6.2293	-0.5543	-1.8625	0.5684	0.523	0.8731	0.001	1.2692	0.3459	-0.4274	-0.6579	-0.0466	-0.1541	0.2668	-1.0902	0.2811	-0.0078	0.2209	1.3289	0.2188	0.4775	-3.7729	16.99	2.903
15	0.0045	0.0319	-0.0405	0.0296	-0.0911	0.1124	0.1587	0.2014	-0.2922	-0.1791	-0.4154	0.111	-0.0842	0.4847	-0.0012	0.3678	0.1196	-0.026	0.6435	0.0029	0.4381	-18.4646	16.4887	7.7712
16	1.0812	1.9633	-0.1935	3.5202	-0.326	0.0288	0.4126	0.2093	0.2258	0.6742	0.5383	0.8509	-1.0192	-0.3479	0.1102	0.5102	-0.0764	-0.101	0.6088	0.1746	0.4851	-11.5546	22.1054	8.7714
17	0.8862	0.2242	0.3338	0.8387	0.1096	0.6194	-0.313	0.0827	-0.0096	0.0341	0.2379	-0.0255	0.0186	-0.0807	-0.0003	0.3657	-0.006	0.0234	0.4282	0.0056	0.399	-4.5704	15.8115	15.7872
18	0.9835	-1.1196	1.2933	1.1546	-1.2549	1.3359	0.0375	0.1623	-0.0903	-0.2557	-0.0229	-0.0608	-0.0874	0.464	-0.0001	0.3967	-0.0311	0.0766	0.3625	-0.0099	0.43	4.7243	13.7226	23.4933

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESID 62 THROUGH 79 )
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESID 80 THROUGH 96 )
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESID 97 THROUGH 115 )
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESID 116 THROUGH 135 )
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESID 136 THROUGH 175 )
6	X-RAY DIFFRACTION	6	CHAIN A AND (RESID 176 THROUGH 191 )
7	X-RAY DIFFRACTION	7	CHAIN C AND (RESID 229 THROUGH 276 )
8	X-RAY DIFFRACTION	8	CHAIN C AND (RESID 277 THROUGH 322 )
9	X-RAY DIFFRACTION	9	CHAIN B AND (RESID 113 THROUGH 125 )
10	X-RAY DIFFRACTION	10	CHAIN B AND (RESID 126 THROUGH 135 )
11	X-RAY DIFFRACTION	11	CHAIN B AND (RESID 136 THROUGH 146 )
12	X-RAY DIFFRACTION	12	CHAIN B AND (RESID 147 THROUGH 155 )
13	X-RAY DIFFRACTION	13	CHAIN B AND (RESID 156 THROUGH 165 )
14	X-RAY DIFFRACTION	14	CHAIN B AND (RESID 166 THROUGH 170 )
15	X-RAY DIFFRACTION	15	CHAIN B AND (RESID 171 THROUGH 180 )
16	X-RAY DIFFRACTION	16	CHAIN B AND (RESID 181 THROUGH 186 )
17	X-RAY DIFFRACTION	17	CHAIN D AND (RESID 247 THROUGH 276 )
18	X-RAY DIFFRACTION	18	CHAIN D AND (RESID 277 THROUGH 320 )

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OUTER MEMBRANE PROTEIN ASSEMBLY FACTOR ... , 4 types, 4 molecules ABCD

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