PDB-6vk7: Crystal Structure of reduced Methylosinus trichosporium OB3b Solu...

ID or keywords:

Entry

Database: PDB / ID: 6vk7

Title

Crystal Structure of reduced Methylosinus trichosporium OB3b Soluble Methane Monooxygenase Hydroxylase

Components

(Methane monooxygenase) x 2
Methane monooxygenase component A alpha chain

Keywords

OXIDOREDUCTASE / Methane Monooxygenase Hydroxylase

Function / homology

Function and homology information

methane metabolic process / methane monooxygenase (soluble) / methane monooxygenase [NAD(P)H] activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / one-carbon metabolic process / monooxygenase activity / metal ion binding
Similarity search - Function

Biological species

Methylosinus trichosporium OB3b (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 2.12 Å

Authors

Jones, J.C. / Banerjee, R. / Shi, K. / Aihara, H. / Lipscomb, J.D.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM118030, GM08347	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM118000, GM118047	United States

Citation

Journal: Biochemistry / Year: 2020
Title: Structural Studies of theMethylosinus trichosporiumOB3b Soluble Methane Monooxygenase Hydroxylase and Regulatory Component Complex Reveal a Transient Substrate Tunnel.
Authors: Jones, J.C. / Banerjee, R. / Shi, K. / Aihara, H. / Lipscomb, J.D.

History

Deposition	Jan 18, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 5, 2020	Provider: repository / Type: Initial release
Revision 1.1	Aug 26, 2020	Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2	Sep 2, 2020	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3	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

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Download

PDBx/mmCIF format	6vk7.cif.gz	544.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6vk7.ent.gz	366.6 KB	Display	PDB format
PDBx/mmJSON format	6vk7.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/vk/6vk7 ftp://data.pdbj.org/pub/pdb/validation_reports/vk/6vk7	HTTPS FTP

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Related structure data

Related structure data	6vk4C 6vk5C 6vk6C 6vk8C 1mhzS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3dx2-d 1qwu-d 3bvw-d 1hxk-d 1tqv-d 6rrn-d 3bvx-d 1qx1-d 2f1a-d 3d50-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	#238 - Oct 2019 Ribonucleotide Reductase similarity (1)

Deposited unit

A: Methane monooxygenase component A alpha chain

B: Methane monooxygenase

C: Methane monooxygenase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	62.458, 290.452, 139.220
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁
Space group name Hall	C2c2
Symmetry operation	#1: x,y,z #2: x,-y,-z #3: -x,y,-z+1/2 #4: -x,-y,z+1/2 #5: x+1/2,y+1/2,z #6: x+1/2,-y+1/2,-z #7: -x+1/2,y+1/2,-z+1/2 #8: -x+1/2,-y+1/2,z+1/2

Components on special symmetry positions

ID	Model	Components
1	1	B-568- HOH

#1: Protein	Methane monooxygenase component A alpha chain Mass: 60031.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Methylosinus trichosporium OB3b (bacteria) References: UniProt: A0A2D2D5X0, UniProt: P27353*PLUS
#2: Protein	Methane monooxygenase Mass: 45295.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Methylosinus trichosporium OB3b (bacteria) References: UniProt: A0A2D2D5X7
#3: Protein	Methane monooxygenase Mass: 19444.400 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Methylosinus trichosporium OB3b (bacteria) References: UniProt: A0A2D2D0T0
#4: Chemical	ChemComp-FE / FE (III) ION Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 736 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.53 Å³/Da / Density % sol: 51.39 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: Tacsimate and PEG3350

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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: Jul 25, 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: 2.12→49.11 Å / Num. obs: 72012 / % possible obs: 99.5 % / Redundancy: 5.1 % / B_iso Wilson estimate: 36.49 Å² / CC_1/2: 0.994 / R_merge(I) obs: 0.161 / Net I/σ(I): 6.7
Reflection shell	Resolution: 2.12→2.16 Å / Num. unique obs: 4337 / CC_1/2: 0.401 / R_pim(I) all: 0.983

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Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
XDS		data reduction
PHENIX		phasing
PHENIX		data processing
PHENIX		data scaling

Refinement

Method to determine structure:

FOURIER SYNTHESIS
Starting model: 1MHZ

1mhz

Resolution: 2.12→49.11 Å / SU ML: 0.2455 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.0356

	R_factor	Num. reflection	% reflection
R_free	0.2033	3609	5.01 %
R_work	0.1623	-	-
obs	0.1644	71966	99.38 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 37.03 Å²

Refinement step

Cycle: LAST / Resolution: 2.12→49.11 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8686	0	2	737	9425

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	8951
X-RAY DIFFRACTION	f_angle_d	0.7728	12164
X-RAY DIFFRACTION	f_chiral_restr	0.0459	1263
X-RAY DIFFRACTION	f_plane_restr	0.0048	1574
X-RAY DIFFRACTION	f_dihedral_angle_d	17.3626	3214

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 (%)
2.12-2.15	0.3154	143	0.2823	2541	X-RAY DIFFRACTION	97.64
2.15-2.18	0.3099	160	0.2708	2572	X-RAY DIFFRACTION	99.42
2.18-2.21	0.3132	155	0.2486	2562	X-RAY DIFFRACTION	99.82
2.21-2.24	0.2573	129	0.2437	2638	X-RAY DIFFRACTION	99.75
2.24-2.28	0.2747	112	0.2498	2624	X-RAY DIFFRACTION	99.85
2.28-2.31	0.2659	143	0.2241	2648	X-RAY DIFFRACTION	99.82
2.31-2.35	0.2988	130	0.2274	2565	X-RAY DIFFRACTION	99.78
2.35-2.4	0.2512	130	0.2192	2672	X-RAY DIFFRACTION	99.79
2.4-2.44	0.3123	138	0.2198	2581	X-RAY DIFFRACTION	99.82
2.44-2.49	0.2444	125	0.2048	2637	X-RAY DIFFRACTION	99.75
2.49-2.55	0.2666	137	0.2013	2610	X-RAY DIFFRACTION	99.64
2.55-2.6	0.2494	121	0.1985	2653	X-RAY DIFFRACTION	99.75
2.6-2.67	0.2526	157	0.1935	2580	X-RAY DIFFRACTION	99.82
2.67-2.74	0.2613	147	0.1898	2637	X-RAY DIFFRACTION	99.78
2.74-2.82	0.2416	147	0.1849	2604	X-RAY DIFFRACTION	99.49
2.82-2.91	0.2526	126	0.1861	2637	X-RAY DIFFRACTION	99.75
2.91-3.02	0.263	130	0.1796	2602	X-RAY DIFFRACTION	99.09
3.02-3.14	0.1751	146	0.1731	2600	X-RAY DIFFRACTION	97.93
3.14-3.28	0.2115	141	0.1643	2632	X-RAY DIFFRACTION	99.39
3.28-3.45	0.2061	145	0.1585	2646	X-RAY DIFFRACTION	99.39
3.45-3.67	0.1692	115	0.1437	2649	X-RAY DIFFRACTION	99.32
3.67-3.95	0.1613	131	0.1197	2662	X-RAY DIFFRACTION	99.57
3.95-4.35	0.1679	153	0.1167	2660	X-RAY DIFFRACTION	99.75
4.35-4.98	0.1552	141	0.1147	2684	X-RAY DIFFRACTION	99.79
4.98-6.27	0.1827	143	0.1334	2657	X-RAY DIFFRACTION	97.32
6.27-49.11	0.1298	164	0.134	2804	X-RAY DIFFRACTION	98.87

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	3.03242130387	-0.714783827787	3.17378562569	0.632080283917	-1.50195889881	8.53446270322	0.0391721972194	0.216676972849	-0.0767326504996	-0.133625465963	-0.0577648738149	-0.125325356068	0.195881790475	0.611895984049	0.0177400484185	0.291981981808	0.0173736382984	0.0338644014639	0.201306140261	-0.0342437246688	0.399167722122	41.8579503567	14.7314704218	16.7046452007
2	0.445704057609	0.0713421388003	0.429904447235	0.348399889817	-0.273765919612	0.874174384667	0.025652555774	0.0949207117694	-0.0548917700376	-0.0541758269531	0.0637214362922	-0.152264742423	0.111459951599	0.110891291043	-0.108157225537	0.29414566876	-0.0465482640289	0.0159265659161	0.263210212614	-0.00487124329014	0.289562297738	33.363390216	37.6878167321	19.9386961043
3	0.336448057886	-0.117575018303	0.0204670672559	1.18626987446	0.17334731965	0.792282266706	-0.00993983084842	0.0941359974998	-0.0126482413769	-0.130365553806	0.0312443841768	-0.236375925845	-0.0634044632899	0.189851493579	-0.0296148529662	0.286889393767	-0.018112614576	0.0175536566252	0.3189981837	-0.00105722191176	0.289498378233	29.9982414966	46.6253018187	9.94852176116
4	9.29001271516	-7.5361164424	-2.95452060923	6.18759139921	2.54752962723	1.4806316424	-0.231608515354	0.133963516198	0.0167284572322	0.107427226868	0.169910981189	-0.485814404081	-0.0257184901985	0.226000371565	0.0566873673843	0.354905708263	-0.0638882128714	-0.000306418831304	0.340508054372	-0.0293026848745	0.425718988475	36.8395858256	54.8344222021	-0.652473686325
5	6.11710906942	1.5329202263	-1.11656048065	0.944410612805	-0.823631402822	1.18011239448	0.0761553708911	-0.109766806347	0.511588660781	0.0380028664763	-0.00820954772542	0.097528465727	-0.273107562696	-0.0164292158213	-0.0638926270874	0.327977594954	0.036513635096	0.00139049957811	0.208967839477	-0.0247619559231	0.236618385706	20.0279352815	71.811515375	8.77303634715
6	0.839620940405	-0.220711572542	-0.555660182548	0.943786635306	-0.0232974414774	1.25558444424	-0.0024152626516	0.0644935206928	-0.0147573289523	-0.0946613632066	-0.0307999176349	0.0278386128047	-0.11322814422	-0.121792321097	0.0223287391443	0.285845680302	0.0325463502257	-0.0323360058819	0.243328450761	-0.00100856209136	0.213427855658	13.0770526361	58.2845274693	-2.08491367768
7	5.23128838446	4.60503244283	3.40678663335	6.04923366494	2.11042053895	2.75190460346	-0.284549673204	-0.0281595731286	0.49785440067	0.0473768278724	0.0712944954565	0.137351790306	-0.244298445238	-0.000640776632466	0.240906004753	0.419457380825	0.0513043173076	0.0147918337823	0.271987741484	0.0211267344778	0.194545062839	22.6682858758	63.953466709	28.6182709257
8	0.330615677459	-0.16252324221	0.162404040845	0.560520126274	-0.197212954648	0.550679499794	0.0130126166123	-0.0098192582498	-0.0810405040978	-0.0210695441263	0.0327125779058	0.0419285581333	0.109894884534	-0.0228902542593	-0.0489208192292	0.265527619811	-0.0106321553831	-0.00465135836987	0.227054365257	-0.020078058023	0.24666435145	22.5654514856	15.907477381	16.9401783334
9	7.71863058087	-0.728242615467	1.75783446967	1.96865901756	2.36560444997	5.6580971031	-0.256250071949	0.395249334899	0.291491126175	-0.265473339186	0.0519354563182	0.328240415836	-0.221045356248	-0.654397312466	0.210561431272	0.452749387407	0.0662826609282	-0.0198359770829	0.434267011954	-0.0340575214411	0.325875726664	-1.27061886042	49.4071954271	-1.83054987663
10	2.26230701691	1.23707584602	0.0490119523246	4.73968581523	4.10061475101	4.30361872816	0.0377205492909	0.172510147405	0.038115397412	-0.107961083993	-0.314707334373	1.3277214155	-0.0588864471762	-0.570837613904	0.268940164863	0.330041173701	0.0255740394515	-0.0347731683252	0.403781300331	-0.0384437525502	0.486669515439	-5.99808876513	34.76669714	-6.83829027422
11	1.23789206534	0.244006812267	-0.337568814375	4.46938852827	-0.18304276473	0.9409510199	0.0709575481266	0.0012971640601	-0.0485492707792	-0.139576555268	-0.0869324887678	0.299380570508	0.0387208405423	-0.227038603453	-0.00295579406955	0.286292042917	0.0067914956111	-0.0502366037752	0.347334919129	-0.0220409757441	0.252026753107	4.09444501676	28.5580177629	-9.45793280387
12	3.88467869278	2.66743455817	-0.00210382313193	7.92689995503	-0.54011447869	0.0534194373771	-0.0609610429126	0.193742999666	-0.0817788480407	-0.804800343077	0.212917928611	-0.437021163615	0.0223977970285	0.324669366849	-0.156365076778	0.415271425985	0.00315380480683	0.0540363534653	0.312486186652	-0.0957107850123	0.330526280462	21.4148499046	22.9284056271	-19.4425044955
13	2.75343381537	2.44781549628	-0.601325912869	3.72606898356	-1.0832468525	0.788570943031	-0.0203477624134	0.190500366282	-0.00196010584528	-0.239057846915	0.0848491134982	-0.0353194882193	-0.107616422344	0.0553791179879	-0.0570265827866	0.307384604786	0.0391030877539	0.0108599996749	0.253175500938	-0.0596734964225	0.215317809726	21.763080864	31.0902405417	-14.2215398799
14	5.02727140342	-3.95203517516	-0.742507753521	3.81572047612	2.4023197973	6.2152970926	0.149030072575	0.424096300024	0.473354209512	-1.23956008233	-0.0166154471375	-0.710352098879	-0.560555327677	0.494710845291	-0.133654763609	0.484765955911	-0.0511739553899	0.0978024381935	0.366610203632	0.0383354801483	0.345762075522	23.1252290592	53.5787545435	-22.0717980523

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 12 through 45 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 46 through 96 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 97 through 315 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 316 through 352 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 353 through 403 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 404 through 526 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 10 through 36 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 37 through 395 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 2 through 10 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 11 through 25 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 26 through 87 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 88 through 104 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 105 through 152 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 153 through 169 )

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Jul 12, 2017. Major update of PDB

-
Yorodumi