PDB-2yh9: Crystal structure of the dimeric BamE from E. coli

ID or keywords:

Entry

Database: PDB / ID: 2yh9

Title

Crystal structure of the dimeric BamE from E. coli

Components

SMALL PROTEIN A

Keywords

MEMBRANE PROTEIN /

LIPOPROTEIN / 3D DOMAIN SWAP

Function / homology

Function and homology information

Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / protein-macromolecule adaptor activity / response to antibiotic /

membrane / identical protein binding
Similarity search - Function

Biological species

ESCHERICHIA COLI (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.8 Å

Authors

Zeth, K. / Albrecht, R.

Citation

Journal: J.Biol.Chem. / Year: 2011
Title: Structural Basis of Outer Membrane Protein Biogenesis in Bacteria.
Authors: Albrecht, R. / Zeth, K.

History

Deposition	Apr 27, 2011	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 29, 2011	Provider: repository / Type: Initial release
Revision 1.1	Aug 10, 2011	Group: Database references / Version format compliance

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2yh9.cif.gz	94 KB	Display	PDBx/mmCIF format
PDB format	pdb2yh9.ent.gz	78.9 KB	Display	PDB format
PDBx/mmJSON format	2yh9.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/yh/2yh9 ftp://data.pdbj.org/pub/pdb/validation_reports/yh/2yh9	HTTPS FTP

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Related structure data

Related structure data	2yh3C 2yh5C 2yh6C 2yhcC C: citing same article (ref.)
Similar structure data	3sys-1 2y2x-2 6yrq-d 2q68-1 2q69-1 3gi7-1 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#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: SMALL PROTEIN A

B: SMALL PROTEIN A

C: SMALL PROTEIN A

29.7 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: SMALL PROTEIN A

B: SMALL PROTEIN A

C: SMALL PROTEIN A

A: SMALL PROTEIN A

B: SMALL PROTEIN A

C: SMALL PROTEIN A

defined by author&software
59.4 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	69.660, 96.520, 50.490
Angle α, β, γ (deg.)	90.00, 134.06, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	B-2024- HOH
2	1	C-2019- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	3	A	10 - 60
2	1	1	3	B	10 - 60
3	1	1	3	C	10 - 60

#1: Protein	SMALL PROTEIN A / BAME PROTEIN Mass: 9907.614 Da / Num. of mol.: 3 / Fragment: RESIDUES 34-113 Source method: isolated from a genetically manipulated source Details: LIPOPROTEIN SMPA/BAME / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A937
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

SMALL PROTEIN A / BAME PROTEIN

Mass: 9907.614 Da / Num. of mol.: 3 / Fragment: RESIDUES 34-113
Source method: isolated from a genetically manipulated source
Details: LIPOPROTEIN SMPA/BAME / Source: (gene. exp.)

ESCHERICHIA COLI (E. coli) / Strain: K-12 / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A937

#2: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.07 Å³/Da / Density % sol: 40.62 % / Description: NONE
Crystal grow	pH: 7.5 / Details: 30% PEG 4000, 10% I-PROH, 0.1 M HEPES PH 7.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.979
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 1.8→50 Å / Num. obs: 21093 / % possible obs: 100 % / Observed criterion σ(I): 2.8 / Redundancy: 5.7 % / R_merge(I) obs: 0.07 / Net I/σ(I): 25.7
Reflection shell	Resolution: 1.8→1.88 Å / R_merge(I) obs: 0.47 / Mean I/σ(I) obs: 2.8 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0102	refinement
XDS		data reduction
XDS		data scaling
SHARP		phasing
DM		phasing
BUCCANEER		phasing

Refinement

Method to determine structure:

SAD
Starting model: NONE

Resolution: 1.8→22.29 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.941 / SU B: 6.828 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.19 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22859	1111	5 %	RANDOM
R_work	0.18121	-	-	-
obs	0.18366	21093	100 %	-

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: 21.797 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.65 Å²	0 Å²	0.69 Å²
2-	-	-0.61 Å²	0 Å²
3-	-	-	-0.07 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→22.29 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1563	0	0	174	1737

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.025	0.022	1613
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.831	1.933	2201
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.511	5	202
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	41.539	24.795	73
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.555	15	255
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.86	15	7
X-RAY DIFFRACTION	r_chiral_restr	0.123	0.2	253
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.021	1231
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.548	1.5	1002
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	2.54	2	1637
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	3.709	3	611
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	5.501	4.5	562
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr	2.502	3	1613
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	203	tight positional	0.11	0.05
2	B	203	tight positional	0.18	0.05
3	C	203	tight positional	0.12	0.05
1	A	193	loose positional	0.13	5
2	B	193	loose positional	0.21	5
3	C	193	loose positional	0.14	5
1	A	203	tight thermal	0.31	0.5
2	B	203	tight thermal	0.29	0.5
3	C	203	tight thermal	0.32	0.5
1	A	193	loose thermal	0.31	10
2	B	193	loose thermal	0.34	10
3	C	193	loose thermal	0.29	10

LS refinement shell

Resolution: 1.8→1.846 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.317	82	-
R_work	0.263	1549	-
obs	-	-	100 %

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	2.0115	-1.2436	-1.6774	1.1589	0.5983	1.896	-0.0894	0.3585	-0.1711	0.0323	-0.1156	0.0449	0.1056	-0.4179	0.205	0.0189	-0.0363	-0.0089	0.1653	-0.0308	0.0564	-18.453	42.84	3.846
2	0.8083	0.4706	-0.9505	0.6069	-0.6875	1.6628	-0.0971	-0.08	-0.1559	-0.0862	-0.0715	-0.0805	0.2323	0.139	0.1686	0.0636	0.0315	0.0047	0.0713	0.0389	0.077	3.094	34.494	8.438
3	3.3036	1.7525	-6.9023	11.3828	-8.4862	16.6572	-0.2011	-0.0746	-0.0021	-0.481	0.0454	-0.3736	0.6106	0.1242	0.1557	0.146	0.0545	0.0714	0.026	0.0202	0.1886	5.571	26.592	6.694
4	1.2885	1.0784	-4.3009	6.3591	2.4684	21.5786	-0.4575	0.5235	-0.0592	-1.7719	0.7043	-0.463	0.149	-1.4969	-0.2468	0.5581	-0.2664	0.1174	0.2286	-0.0385	0.067	-7.014	63.104	-18.952
5	0.2456	0.0414	-0.0983	0.4367	-0.569	1.4973	0.0147	-0.0096	0.042	0.0609	-0.0175	0.0408	-0.1218	-0.0305	0.0029	0.0486	0.0069	-0.0288	0.0425	-0.001	0.053	-1.801	57.829	5.486
6	0.2308	-0.2999	-0.4168	22.7676	-1.8675	1.0636	-0.0427	-0.0844	-0.0993	0.9078	-0.1281	0.1735	-0.0794	0.1132	0.1708	0.1619	0.0402	0.0375	0.1845	0.013	0.0559	-3.684	57.233	19.443
7	32.7015	0	-7.0482	9.7256	0	26.9508	0.9388	0.1595	0.4349	0.5899	-0.1237	-0.7403	-0.6887	0.4029	-0.8152	0.0917	0.0148	-0.0141	0.0675	0.0461	0.2055	7.75	30.005	18.032
8	1.6761	-2.0913	0.3154	3.0099	-0.5453	0.1187	-0.0897	0.0347	-0.1655	0.052	0.0383	-0.0038	0.0102	-0.0231	0.0513	0.0668	-0.0231	0.0346	0.0832	-0.0133	0.1452	-1.829	37.277	14.462
9	1.0054	0.9284	-1.3657	1.1162	-1.0656	2.0798	-0.0007	0.106	0.0336	0.0527	-0.0102	0.058	-0.0096	-0.2458	0.0109	0.0491	0.0104	-0.016	0.1215	0.0168	0.0703	-15.194	51.154	4.904

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	7 - 28
2	X-RAY DIFFRACTION	2	A	29 - 64
3	X-RAY DIFFRACTION	3	A	65 - 70
4	X-RAY DIFFRACTION	4	B	4 - 11
5	X-RAY DIFFRACTION	5	B	12 - 64
6	X-RAY DIFFRACTION	6	B	65 - 72
7	X-RAY DIFFRACTION	7	C	5 - 11
8	X-RAY DIFFRACTION	8	C	12 - 32
9	X-RAY DIFFRACTION	9	C	33 - 71

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