PDB-6in8: Crystal structure of MucB

ID or keywords:

Entry

Database: PDB / ID: 6in8

Title

Crystal structure of MucB

Components

Sigma factor AlgU regulatory protein MucB

Keywords

MEMBRANE PROTEIN / Outer membrane protein

Function / homology

Function and homology information

regulation of polysaccharide biosynthetic process / antisigma factor binding / alginic acid biosynthetic process / outer membrane-bounded periplasmic space
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Li, S. / Zhang, Q. / Bartlam, M.

Funding support

China, 1items

Citation

Journal: Febs J. / Year: 2019
Title: Structural basis for the recognition of MucA by MucB and AlgU in Pseudomonas aeruginosa.
Authors: Li, S. / Lou, X. / Xu, Y. / Teng, X. / Liu, R. / Zhang, Q. / Wu, W. / Wang, Y. / Bartlam, M.

History

Deposition	Oct 24, 2018	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 24, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jan 8, 2020	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Nov 22, 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6in8.cif.gz	126 KB	Display	PDBx/mmCIF format
PDB format	pdb6in8.ent.gz	97.3 KB	Display	PDB format
PDBx/mmJSON format	6in8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6in8_validation.pdf.gz	417.5 KB	Display	wwPDB validaton report
Full document	6in8_full_validation.pdf.gz	420.7 KB	Display
Data in XML	6in8_validation.xml.gz	13 KB	Display
Data in CIF	6in8_validation.cif.gz	17.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/in/6in8 ftp://data.pdbj.org/pub/pdb/validation_reports/in/6in8	HTTPS FTP

-
Related structure data

Related structure data	6in7C 6in9C 2p4bS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6pnm-d 1mgp-d 5ueh-d 1l9k-d 6pno-d 4zi1-d 6ilq-d 4ysp-d 2pxa-2 3kuv-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

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Sigma factor AlgU regulatory protein MucB

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

1

Idetical with deposited unit
defined by author
Evidence: equilibrium centrifugation

Unit cell

Length a, b, c (Å)	69.076, 69.076, 223.103
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	179
Space group name H-M	P6₅22

Components on special symmetry positions

ID	Model	Components
1	1	A-426- HOH

#1: Protein	Sigma factor AlgU regulatory protein MucB Mass: 32738.725 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: mucB, algN, PA0764 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P38108
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Sigma factor AlgU regulatory protein MucB

Mass: 32738.725 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Pseudomonas aeruginosa (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: mucB, algN, PA0764 / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P38108

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.35 Å³/Da / Density % sol: 47.58 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 2 M Ammonium dibasic phosphate, 0.1 M Tris pH 8.5

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97853 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 30, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97853 Å / Relative weight: 1
Reflection	Resolution: 2.2→50 Å / Num. obs: 16960 / % possible obs: 100 % / Redundancy: 37 % / R_pim(I) all: 0.025 / Net I/σ(I): 38.5
Reflection shell	Resolution: 2.2→2.24 Å / Redundancy: 15 % / Mean I/σ(I) obs: 4.5 / Num. unique obs: 813 / R_pim(I) all: 0.138 / % possible all: 100

-
Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2P4B

2p4b

Resolution: 2.2→40.795 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.48

	R_factor	Num. reflection	% reflection
R_free	0.2407	842	4.99 %
R_work	0.1864	-	-
obs	0.1892	16885	99.99 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.2→40.795 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2137	0	0	120	2257

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	2180
X-RAY DIFFRACTION	f_angle_d	1.083	2957
X-RAY DIFFRACTION	f_dihedral_angle_d	14.518	800
X-RAY DIFFRACTION	f_chiral_restr	0.042	326
X-RAY DIFFRACTION	f_plane_restr	0.005	394

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 (%)
2.2-2.3379	0.2753	150	0.2067	2561	X-RAY DIFFRACTION	100
2.3379-2.5184	0.2847	119	0.2146	2620	X-RAY DIFFRACTION	100
2.5184-2.7717	0.2817	117	0.2186	2648	X-RAY DIFFRACTION	100
2.7717-3.1727	0.2685	144	0.2145	2648	X-RAY DIFFRACTION	100
3.1727-3.9967	0.235	153	0.1688	2678	X-RAY DIFFRACTION	100
3.9967-40.8018	0.2085	159	0.1676	2888	X-RAY DIFFRACTION	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	1.3629	-0.6515	0.002	7.0306	-5.1322	4.7775	-0.0911	0.4059	-0.1212	-0.7925	-0.0378	-0.0416	1.9706	-0.1306	0.27	0.683	-0.0491	0.1014	0.315	-0.0786	0.2959	40.514	38.4848	12.4041
2	1.9201	-0.0541	-1.0388	2.2695	-1.2374	3.6768	-0.1455	0.1359	-0.0136	-0.2816	0.0444	-0.1426	0.4805	-0.037	0.1475	0.256	-0.0675	0.0992	0.2519	0.0292	0.2883	38.0698	37.7193	33.0285
3	3.2056	1.9657	2.4175	4.3883	1.6214	3.7224	-0.101	0.111	-0.2543	-0.3918	-0.0629	0.1231	0.8049	-0.7464	0.1019	0.5294	-0.1346	0.1737	0.2897	-0.0013	0.3167	33.6086	29.6316	34.5165
4	4.4118	-3.0208	-2.6789	5.8289	0.6099	3.7518	0.0405	0.0969	-0.1751	0.1986	-0.3428	0.428	0.3035	-0.1348	0.3024	0.3877	-0.1489	0.0426	0.6386	-0.059	0.3595	24.8287	33.4462	35.1734
5	1.9424	-0.6911	0.5604	1.1894	-0.3352	2.633	-0.0925	0.1054	0.0402	-0.1248	-0.084	0.0246	0.41	-0.3389	0.2313	0.2843	-0.0372	0.1289	0.2741	0.0073	0.3203	37.6814	44.4251	18.2743
6	1.372	-0.1993	0.2018	0.9984	-1.0497	3.3963	-0.1162	0.0107	0.051	-0.1344	-0.0103	0.0017	0.0972	-0.0848	0.1547	0.2054	-0.0551	0.0616	0.198	0.0246	0.2665	37.4495	47.5049	23.5174
7	1.1801	-0.0551	1	1.4735	-1.1877	2.9289	0.1814	-0.9153	-0.3796	-0.2774	-0.1898	-0.0081	0.6835	-0.054	-0.0676	0.6223	-0.1104	0.173	0.342	0.0135	0.5098	34.3928	25.0073	36.3573
8	1.9333	0.247	-0.7018	2.066	-0.4112	1.8126	-0.6454	0.1853	-0.9426	0.0684	0.1438	0.2398	0.5574	-0.9937	0.2365	0.3942	-0.0866	0.0986	0.5795	0.0505	0.4503	15.6217	39.5118	24.6243
9	3.5227	1.8252	-2.2597	2.5092	-2.169	2.8346	-0.1173	-0.3742	-0.2577	0.0834	-0.0029	0.1687	0.4602	-0.5012	0.3211	0.2651	-0.1512	0.0764	0.4868	-0.0114	0.3352	19.4598	40.8251	26.6619
10	2.6643	1.4417	-0.6728	0.7561	-0.3688	0.1697	0.1617	-1.598	-0.3468	0.349	-0.2128	0.3134	-0.4008	-1.0012	0.0146	0.3559	0.0039	0.0668	1.0838	-0.0248	0.5299	12.2799	47.2673	38.0149
11	5.1802	1.2535	-1.0234	1.4074	-0.6231	0.9012	-0.1607	-0.1171	0.078	0.0684	0.031	0.1578	0.0604	-0.9574	0.027	0.2236	-0.0342	0.0584	0.6748	-0.0277	0.3153	12.7455	46.877	27.1193

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 18 through 37 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 38 through 61 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 62 through 84 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 85 through 102 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 103 through 141 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 142 through 182 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 183 through 213 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 214 through 239 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 240 through 258 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 259 through 283 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 284 through 311 )

-
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://pdbjlvh1.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