PDB-6u76: Structure of methanesulfinate monooxygenase MsuC from Pseudomonas...

ID or keywords:

Entry

Database: PDB / ID: 6u76

Title

Structure of methanesulfinate monooxygenase MsuC from Pseudomonas fluorescens.

Components

methanesulfinate monooxygenase

Keywords

FLAVOPROTEIN / two-component flavin-dependent monooxygenase / methyl sulfur assimilation / dimethylsulfide / global sulfur cycle

Function / homology

Function and homology information

3-methylbutanoyl-CoA dehydrogenase activity / L-leucine catabolic process / flavin adenine dinucleotide binding
Similarity search - Function

Biological species

Pseudomonas fluorescens Pf0-1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Soule, J. / Gnann, A.D. / Parker, M.J. / McKenna, K.C. / Nguyen, S.V. / Phan, N.T. / Wicht, D.K. / Dowling, D.P.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: To be published
Authors: Soule, J. / Gnann, A.D. / Parker, M.J. / McKenna, K.C. / Nguyen, S.V. / Phan, N.T. / Wicht, D.K. / Dowling, D.P.

History

Deposition	Aug 31, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 11, 2020	Provider: repository / Type: Initial release
Revision 1.1	Oct 11, 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	6u76.cif.gz	378.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6u76.ent.gz	256.6 KB	Display	PDB format
PDBx/mmJSON format	6u76.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/u7/6u76 ftp://data.pdbj.org/pub/pdb/validation_reports/u7/6u76	HTTPS FTP

-
Related structure data

Related structure data	5xb8S S: Starting model for refinement
Similar structure data	6uug-1 5xdc-d 5xde-d 4zxv-d 2rfq-d 4w9u-d 3x0y-1 3d6b-d 3x0y-2 4zyj-d 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

Deposited unit

A: methanesulfinate monooxygenase

B: methanesulfinate monooxygenase

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

1

A: methanesulfinate monooxygenase

B: methanesulfinate monooxygenase

A: methanesulfinate monooxygenase

B: methanesulfinate monooxygenase

defined by author&software
Evidence: gel filtration, MsuC runs as a species of similar size to gamma globulin (150 kDa). The expected MW of the tetramer is ~180 kDa, therefore MsuC runs as a more compact structure by gel filtration.
185 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	80.554, 162.411, 61.285
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2
Space group name Hall	P22ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x+1/2,y+1/2,-z #4: -x,-y,z

#1: Protein	methanesulfinate monooxygenase Mass: 46258.012 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens Pf0-1 (bacteria) Strain: Pf0-1 / Gene: Pfl01_3917 / Plasmid: pPfl01_msuC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q3K9A0
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.28 Å³/Da / Density % sol: 45.95 % / Description: trapezoidal shaped, small crystals
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris (pH 8.5) 0.1 M MgCl2 15% (w/v) PEG 3350

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 1, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 2.1→46.7 Å / Num. obs: 47163 / % possible obs: 99.2 % / Redundancy: 9.5 % / CC_1/2: 0.996 / R_pim(I) all: 0.027 / R_rim(I) all: 0.085 / R_sym value: 0.081 / Χ²: 0.891 / Net I/σ(I): 26.7
Reflection shell	Resolution: 2.1→2.18 Å / Redundancy: 7.9 % / Mean I/σ(I) obs: 1.14 / Num. unique obs: 4625 / CC_1/2: 0.868 / R_pim(I) all: 0.307 / R_rim(I) all: 0.91 / R_sym value: 0.853 / Χ²: 0.691 / % possible all: 98.8

-
Processing

Software

Name	Version	Classification
PHENIX	1.15.2_3472	refinement
HKL-2000	2.3.12	data reduction
HKL-2000	2.3.12	data scaling
PHASER	2.5.6	phasing
Coot	0.8.9.1	model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5XB8

5xb8

Resolution: 2.1→46.7 Å / Cross valid method: FREE R-VALUE
Details: Rounds of simulated annealing, minimization, and B-factor refinement were conducted until convergence. TLS refinement was added in the final stages of refinement.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2155	2354	5 %	Random selection
R_work	0.1856	-	-	-
obs	0.1871	44694	98.92 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 61.25 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→46.7 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5964	0	0	182	6146

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0015	6159
X-RAY DIFFRACTION	f_angle_d	0.3964	8392
X-RAY DIFFRACTION	f_chiral_restr	0.0538	929
X-RAY DIFFRACTION	f_plane_restr	0.0031	1089
X-RAY DIFFRACTION	f_dihedral_angle_d	17.4202	2174

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 (%)
2.1-2.17	0.3893	189	0.3115	3575	X-RAY DIFFRACTION	96.89
2.17-2.24	0.3059	192	0.2841	3667	X-RAY DIFFRACTION	98.75
2.24-2.31	0.2911	193	0.2666	3648	X-RAY DIFFRACTION	98.44
2.31-2.41	0.2906	189	0.2323	3602	X-RAY DIFFRACTION	96.61
2.41-2.52	0.2576	196	0.2197	3717	X-RAY DIFFRACTION	99.64
2.52-2.65	0.253	195	0.2277	3705	X-RAY DIFFRACTION	99.87
2.65-2.82	0.2698	197	0.2107	3736	X-RAY DIFFRACTION	99.77
2.82-3.03	0.2669	197	0.2034	3748	X-RAY DIFFRACTION	99.97
3.03-3.34	0.2226	199	0.1963	3773	X-RAY DIFFRACTION	100
3.34-3.82	0.2114	197	0.1828	3739	X-RAY DIFFRACTION	98.38
3.82-4.81	0.1713	201	0.1474	3824	X-RAY DIFFRACTION	99.88
4.81-46.72	0.1707	209	0.1565	3960	X-RAY DIFFRACTION	98.89

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	0.543440584468	-0.927310469478	-0.411860053776	2.04409583721	-0.00498781059037	1.86170146553	-0.165259072854	-0.211953662804	-0.0264274021213	0.130363908481	0.478034042182	0.993091052559	-0.0314317167132	-0.0938766294193	-0.278440767651	0.447608151049	0.023334986824	0.122325645097	0.628719340252	0.0406958686887	0.686131224146	-31.5376657698	15.2264284077	-5.39134181494
2	2.1509856713	-0.506880556569	0.703961647601	3.33687609999	-1.75446814826	3.74967071818	0.0516077390992	-0.260924396302	-0.0742900725458	0.0322225577811	0.1560951747	0.769613042291	-0.0935187673896	-0.372126276171	-0.208355298993	0.341113699972	0.054577984001	0.00827277679	0.465243113157	-0.0417616702363	0.61013761084	-28.5246936511	21.1062597845	-17.3339511376
3	0.952307955345	0.890631111738	0.246277824491	7.23028005712	3.86950317167	5.7780030458	0.115720399451	0.381849775385	0.0515295183392	-0.71715487542	-0.163337490276	0.405756714071	-0.294343463789	-0.341790043951	0.0241474619378	0.476879526222	0.1027525689	-0.167194728418	0.633164837663	0.0075617126312	0.71626398045	-32.8539086562	18.9629169816	-34.3681899108
4	6.69962886692	-0.0380338829909	-4.98790887863	1.94991903445	0.157752413402	3.71548219751	0.0223338080234	-0.172401809579	-0.848729027319	0.0685191254539	-0.0607459145396	0.371725477811	0.915625229264	-0.608127915482	-0.0292496446603	0.603861150819	0.0591120447707	-0.179865697947	0.643322871695	-0.071519522159	0.922535353265	-32.22005087	11.9142063643	-30.249422488
5	1.84027880375	1.27694827783	1.1020747632	3.63296504742	-2.00208785372	3.31739751543	-0.125428893324	-0.304731172827	-0.440384413003	-0.128340653744	0.131703934838	0.026480141844	0.36278575871	-0.0530718648792	-0.0446709054951	0.525676660277	0.0607539631265	-0.155898368367	0.523090927684	-0.1061541365	0.852055358085	-33.3776765197	9.52442351106	-34.4061874718
6	1.23114876167	-0.478024584935	1.01850977791	1.35312126153	-0.363971348852	2.22887480373	0.222869233662	0.113751683628	-0.122364329623	-0.215114710677	0.0194521670852	0.379420352566	0.0984603294704	-0.178813694248	-0.268152435431	0.402878627197	0.0237449180494	-0.0331690150833	0.439469684606	-0.00907526284611	0.59272611177	-23.6727620253	13.4908171558	-21.3734245005
7	7.17388316985	2.62284588585	-2.23141823833	7.02684025013	-1.18766640816	9.54931027647	0.254772165906	-0.410343843106	-0.636820155721	0.348672102827	0.37489006613	0.815649549075	1.22442346568	-0.265595616018	-0.594703890817	1.0034520594	-0.151089904715	-0.101798109843	0.766789379302	0.207388491984	0.650707603214	-10.8961105357	-2.05902972141	13.4970145913
8	0.754240003304	-0.200497402056	0.617950966462	3.41096919743	-2.49779679468	5.32835450643	0.132459073413	-0.0781307058765	0.139460024154	0.0314261000344	-0.13024152727	-0.00904625817016	0.0975274740311	0.183400737737	-0.00992763101361	0.330032238422	-0.00840221255099	0.0310522637588	0.395704357803	-0.0485449116034	0.470383099815	-9.66739343682	15.0830145334	-12.4542944859
9	4.85306641404	0.420914628751	-3.17030959732	3.48058919226	-0.0551398886163	9.4264102822	0.112438588429	0.0195665889149	-0.112005081378	0.235458503419	-0.0133461703918	0.456836664973	-0.112176940631	-0.370365243362	-0.121561711183	0.386706752467	-0.00382025803979	-0.0320715771603	0.420029775186	0.0396838057222	0.658943931792	-20.5462586633	0.406158546324	-9.73631058003
10	5.89942536701	-1.42647606453	3.5170686629	5.74813052065	-2.23887293059	7.82255559325	0.200391040074	0.0412485727553	-0.0393288807505	-0.240818879603	-0.0987918466058	0.590463800691	0.412500356401	-0.434378291116	-0.084551088612	0.571386180038	0.108737454252	0.0536676824423	0.493879646674	-0.0310276447126	0.45186328052	-4.37218314136	12.9863349037	-28.6522369379
11	4.57645487584	-3.76971655254	0.689461870056	7.72151504196	-0.316171928977	4.45625086594	0.158593691883	0.409753454445	-0.275120180983	-0.794588844951	0.0368213914487	0.953149742629	0.215221523928	-0.0918152150954	-0.175055027473	0.503312792413	-0.163509897701	-0.0796757679354	0.632602708768	-0.04207985928	0.708694809196	-22.0236056881	-27.1834004685	-15.0376959323
12	1.47382067155	0.462054750006	0.0883975869522	2.59238497294	-1.26917858519	2.96203783328	-0.114497338716	0.14411781731	-0.17465393357	-0.187741479151	0.11637748736	0.552511165343	0.452214539416	-0.375965630201	-0.0251856765262	0.457129156717	-0.0874970304108	0.0162764958759	0.421115392365	-0.0327399221716	0.619807184621	-17.2619653669	-31.2032062768	-2.68789061105
13	1.77397716328	-0.975660065613	0.00504575536787	3.68699546917	0.917610721478	3.71919814165	-0.172912536827	-0.219190303601	-0.0040704007395	0.329711269464	0.0292248845035	0.547428667908	-0.0998065853045	-0.242365604814	0.145436858491	0.506560023647	-0.0768838959198	0.178699053038	0.528293438514	0.0707736499036	0.805408804251	-22.4305062222	-28.4335352061	14.2067954568
14	0.830182453698	-0.401853713968	-0.95989411775	1.51701766599	-1.514859403	2.46876023914	-0.0188543412838	0.0204249473178	0.0105771287316	0.207093768605	0.180003294146	0.550039408172	-0.0893385149205	-0.33578443381	-0.166680740304	0.501840574793	-0.0687766857363	0.0542199212448	0.466791592853	-0.0407831729909	0.72120546761	-18.9652643731	-22.3174507645	3.77471620216
15	6.59861046563	0.168206084985	5.61241926258	2.10745232354	-2.13951688554	7.25556561668	-0.394989562849	0.51387238385	0.698011796824	-0.639710429213	-0.0717574641583	0.435397897462	-1.28919587348	-0.184230236015	0.430445545356	0.969558999373	0.199924501257	0.107562076845	0.940614165893	0.123459859094	0.746079575749	-10.306592972	-2.38237380977	-33.6701239766
16	1.01909925485	-1.00262651629	0.389606117123	3.7330661261	-2.31294327681	4.49133653449	0.0464823157241	0.141855711354	-0.193509359666	-0.11083316628	-0.151293563496	0.0738558246412	-0.0178829469205	0.133841169545	0.104378821907	0.299425139415	-0.0285556020723	-0.00890617649763	0.367698616849	-0.042484976363	0.423706758339	-2.44877169551	-17.8338920916	-7.46101329576
17	4.66849437733	-0.555194123917	2.87225257636	4.3581353525	0.313614724448	8.6623042563	0.102635587399	0.0440523441387	-0.256698836574	-0.267249272279	-0.0663548552581	0.391311846496	0.288849471048	-0.620193045856	-0.0760452175344	0.316790848683	-0.029510583727	-0.0284311808207	0.369778167113	0.00458370788691	0.527456598267	-18.4573772545	-9.02565388642	-10.1100596847
18	2.88190177654	0.27087633855	-1.9455522989	6.77120103569	-4.39190017811	3.96737531268	-0.0533218816368	-0.486954245729	0.0586752741993	0.553790244912	0.0582969476965	0.423968141979	-0.171331284213	-0.189878794619	0.054850673485	0.656640069801	-0.0579077452985	-0.0330892114482	0.511664112568	-0.0363043846392	0.491005263713	1.36704110746	-13.6287615143	8.57163768038

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 9 through 33 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 34 through 99 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 100 through 145 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 146 through 163 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 164 through 189 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 190 through 257 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 258 through 273 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 274 through 345 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 346 through 371 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 372 through 395 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 9 through 33 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 34 through 99 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 100 through 169 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 170 through 257 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 258 through 273 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 274 through 345 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 346 through 371 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 372 through 395 )

-
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