PDB-2yh6: Structure of the N-terminal domain of BamC from E. coli

ID or keywords:

Entry

Database: PDB / ID: 2yh6

Title

Structure of the N-terminal domain of BamC from E. coli

Components

LIPOPROTEIN 34

Keywords

LIPID BINDING PROTEIN

Function / homology

Function and homology information

Bam protein complex / protein insertion into membrane / Gram-negative-bacterium-type cell outer membrane assembly / cell surface / identical protein binding / membrane
Similarity search - Function

Biological species

ESCHERICHIA COLI (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MIRAS / Resolution: 1.55 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	May 25, 2011	Provider: repository / Type: Initial release
Revision 1.1	Aug 10, 2011	Group: Database references / Version format compliance
Revision 1.2	May 8, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2yh6.cif.gz	186.8 KB	Display	PDBx/mmCIF format
PDB format	pdb2yh6.ent.gz	150.7 KB	Display	PDB format
PDBx/mmJSON format	2yh6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	2yh6_validation.pdf.gz	464.5 KB	Display	wwPDB validaton report
Full document	2yh6_full_validation.pdf.gz	485.7 KB	Display
Data in XML	2yh6_validation.xml.gz	21.9 KB	Display
Data in CIF	2yh6_validation.cif.gz	29.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yh/2yh6 ftp://data.pdbj.org/pub/pdb/validation_reports/yh/2yh6	HTTPS FTP

-
Related structure data

Related structure data	2yh3C 2yh5C 2yh9C 2yhcC C: citing same article (ref.)
Similar structure data	2ye2-d 3g75-2 5cty-1 1z9d-2 5d6p-1 3lhi-d 5aoj-2 5j6m-d 5ctw-1 4qdo-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
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: LIPOPROTEIN 34

B: LIPOPROTEIN 34

C: LIPOPROTEIN 34

D: LIPOPROTEIN 34

hetero molecules

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

1

C: LIPOPROTEIN 34

D: LIPOPROTEIN 34

hetero molecules

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

2

A: LIPOPROTEIN 34

B: LIPOPROTEIN 34

hetero molecules

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

Unit cell

Length a, b, c (Å)	46.577, 46.631, 60.208
Angle α, β, γ (deg.)	102.70, 92.86, 118.20
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	2	A	4 - 113
2	1	1	2	B	4 - 113
3	1	1	2	C	4 - 113
4	1	1	2	D	4 - 113

#1: Protein	LIPOPROTEIN 34 / BAMC Mass: 12532.893 Da / Num. of mol.: 4 / Fragment: N-TERMINAL DOMAIN, RESIDUES 101-212 Source method: isolated from a genetically manipulated source Details: DOMAIN WAS IDENTIFIED BY LIMITED PROTEOLYSIS / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A903
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	THE DOMAIN WAS IDENTIFIED BY LIMITED PROTEOLYSIS. THEREFORE, THE N- AND C-TERMINUS ARE NOT DEFINED.

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.21 Å³/Da / Density % sol: 44.24 % / Description: NONE
Crystal grow	pH: 3.5 / Details: 2 M (NH4)2SO4, 0.1 M CITRIC ACID PH 3.5

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
Detector	Type: DECTRIS PILATUS 6M / 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: 1.55→40 Å / Num. obs: 56570 / % possible obs: 95.1 % / Observed criterion σ(I): 2.7 / Redundancy: 3.4 % / R_merge(I) obs: 0.06 / Net I/σ(I): 11.1
Reflection shell	Resolution: 1.55→1.59 Å / R_merge(I) obs: 0.44 / Mean I/σ(I) obs: 2.7 / % possible all: 93.8

-
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:

MIRAS
Starting model: NONE

Resolution: 1.55→30 Å / Cor.coef. F_o:F_c: 0.954 / Cor.coef. F_o:F_c free: 0.943 / SU B: 3.907 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2343	2994	5 %	RANDOM
R_work	0.19479	-	-	-
obs	0.19676	56570	95.82 %	-

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: 15.031 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.37 Å²	-0.14 Å²	0.1 Å²
2-	-	-0.29 Å²	0.1 Å²
3-	-	-	0.58 Å²

Refinement step

Cycle: LAST / Resolution: 1.55→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3376	0	30	136	3542

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.028	0.022	3483
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	2.53	1.948	4744
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.433	5	437
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.043	25.68	169
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.684	15	592
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	23.453	15	21
X-RAY DIFFRACTION	r_chiral_restr	0.178	0.2	542
X-RAY DIFFRACTION	r_gen_planes_refined	0.013	0.021	2617
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	2.43	1.5	2165
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	3.57	2	3482
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	5.422	3	1318
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	7.542	4.5	1256
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	3.037	3	3483
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	134	tight positional	0.14	0.05
2	B	134	tight positional	0.15	0.05
3	C	134	tight positional	0.15	0.05
4	D	134	tight positional	0.13	0.05
1	A	118	medium positional	0.3	0.5
2	B	118	medium positional	0.25	0.5
3	C	118	medium positional	0.28	0.5
4	D	118	medium positional	0.24	0.5
1	A	134	tight thermal	0.43	0.5
2	B	134	tight thermal	0.44	0.5
3	C	134	tight thermal	0.44	0.5
4	D	134	tight thermal	0.43	0.5
1	A	118	medium thermal	0.41	2
2	B	118	medium thermal	0.37	2
3	C	118	medium thermal	0.43	2
4	D	118	medium thermal	0.42	2

LS refinement shell

Resolution: 1.55→1.59 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.285	237	-
R_work	0.232	4018	-
obs	-	-	93.48 %

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	7.9865	-3.2454	-1.3647	12.9444	0.3136	5.6511	0.2261	-0.6974	0.6313	0.5279	-0.1532	0.1409	-0.5093	-0.0994	-0.0729	0.1328	-0.0641	0.0116	0.2901	-0.0955	0.1245	4.2325	8.3856	8.0486
2	5.0074	-0.5374	-2.2777	2.3105	0.3628	4.3567	0.1143	0.1778	0.639	-0.0739	-0.0436	0.2117	-0.1594	-0.5218	-0.0708	0.0414	-0.0104	-0.0156	0.284	0.0047	0.1366	-8.2924	6.0804	1.7446
3	1.8586	-0.2821	-0.6356	1.4252	0.1199	1.5672	-0.017	0.0117	-0.0205	-0.0751	-0.0245	-0.0335	0.0749	-0.0315	0.0415	0.0628	-0.0178	-0.0054	0.1049	0.0061	0.0405	1.9224	-1.701	-1.9845
4	6.337	-2.716	-1.8081	11.1178	0.4329	5.966	0.041	-0.5227	-0.305	0.3493	-0.2405	-0.3295	0.6324	0.0368	0.1995	0.1058	-0.0571	-0.0221	0.2438	0.0752	0.1232	14.019	-2.1263	6.3011
5	6.626	-1.1852	1.4755	3.8213	1.0109	5.0138	0.1707	0.3891	-0.0818	-0.0352	0.0542	-0.2932	0.1872	0.5209	-0.2249	0.019	-0.0281	-0.0103	0.3556	0.0086	0.069	26.5326	2.3541	1.2951
6	2.7452	-0.5135	0.1036	2.4206	0.2595	1.3304	0.0331	0.0309	0.1956	-0.1082	-0.0554	-0.0339	-0.1093	0.0639	0.0223	0.0768	-0.0295	0.004	0.1398	0.0058	0.0784	16.7682	10.7338	0.6835
7	22.9555	6.1517	3.8051	7.0673	1.8879	4.5613	0.1274	0.6892	-0.66	-0.3671	0.1193	-0.6825	-0.3106	0.4639	-0.2467	0.3192	0.041	0.0669	0.0806	-0.0031	0.1487	10.5468	-20.3555	23.0152
8	5.0324	-2.141	0.2662	4.9619	1.6272	5.36	-0.0468	-0.2414	-0.1869	0.271	0.3121	0.0337	0.3734	0.374	-0.2653	0.3382	0.1318	-0.0043	0.0791	0.0034	0.0335	11.9895	-33.8217	27.6709
9	2.4458	-0.6259	0.2506	1.9369	0.4425	1.2436	0.0013	-0.1223	-0.1471	0.0077	-0.0412	0.184	0.0768	-0.086	0.0399	0.145	0.0127	0.0028	0.0679	0.0074	0.0845	-0.0227	-28.7132	28.2826
10	12.0699	0.6437	2.202	6.0254	0.1241	4.2114	-0.2047	0.458	-0.2402	-0.9804	0.0526	0.6314	0.0769	-0.3481	0.1521	0.3894	0.0675	-0.1039	0.105	-0.0357	0.1364	-4.3051	-16.9329	20.7512
11	2.4848	-1.0905	1.0944	4.6324	-1.3284	4.188	-0.0527	-0.0972	-0.0788	0.0001	0.0452	0.5921	-0.3438	-0.3842	0.0074	0.2505	0.1162	-0.0273	0.0808	-0.029	0.1128	-7.6479	-4.6816	27.3225
12	1.7416	-0.181	0.5063	1.4645	-0.2612	1.5381	0.01	-0.0708	-0.0193	0.0097	-0.051	0.0023	-0.0579	0.035	0.041	0.1074	0.0094	0.0084	0.056	0.0008	0.0378	3.7335	-9.9918	30.8417

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	77 - 91
2	X-RAY DIFFRACTION	2	A	92 - 114
3	X-RAY DIFFRACTION	3	A	115 - 187
4	X-RAY DIFFRACTION	4	B	77 - 91
5	X-RAY DIFFRACTION	5	B	92 - 114
6	X-RAY DIFFRACTION	6	B	115 - 188
7	X-RAY DIFFRACTION	7	C	77 - 91
8	X-RAY DIFFRACTION	8	C	92 - 114
9	X-RAY DIFFRACTION	9	C	115 - 187
10	X-RAY DIFFRACTION	10	D	77 - 91
11	X-RAY DIFFRACTION	11	D	92 - 114
12	X-RAY DIFFRACTION	12	D	115 - 188

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi