PDB-6m1w: Structure of the 2-Aminoisobutyric acid Monooxygenase Hydroxylase

ID or keywords:

Entry

Database: PDB / ID: 6m1w

Title

Structure of the 2-Aminoisobutyric acid Monooxygenase Hydroxylase

Components

(Amidohydrolase) x 2

Keywords

OXIDOREDUCTASE / Monooxygenase / Hydroxylase

Function / homology

Function and homology information

secondary metabolic process / carboxy-lyase activity / hydrolase activity / metal ion binding / cytoplasm
Similarity search - Function

Biological species

Rhodococcus wratislaviensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.75 Å

Authors

Hibi, M. / Mikami, B. / Ogawa, J.

Citation

Journal: Commun Biol / Year: 2021
Title: A three-component monooxygenase from Rhodococcus wratislaviensis may expand industrial applications of bacterial enzymes.
Authors: Hibi, M. / Fukuda, D. / Kenchu, C. / Nojiri, M. / Hara, R. / Takeuchi, M. / Aburaya, S. / Aoki, W. / Mizutani, K. / Yasohara, Y. / Ueda, M. / Mikami, B. / Takahashi, S. / Ogawa, J.

History

Deposition	Feb 26, 2020	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jan 6, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jan 27, 2021	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Nov 13, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6m1w.cif.gz	358.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6m1w.ent.gz	243.6 KB	Display	PDB format
PDBx/mmJSON format	6m1w.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6m1w_validation.pdf.gz	473.8 KB	Display	wwPDB validaton report
Full document	6m1w_full_validation.pdf.gz	490.5 KB	Display
Data in XML	6m1w_validation.xml.gz	29.2 KB	Display
Data in CIF	6m1w_validation.cif.gz	39.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/m1/6m1w ftp://data.pdbj.org/pub/pdb/validation_reports/m1/6m1w	HTTPS FTP

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Related structure data

Related structure data	6m2iC C: citing same article (ref.)
Similar structure data	6m2i-1 3l84-1 1jqb-d 3fpl-1 3jv7-d 1ped-d 1ea0-1 5xvt-1 2cg2-1 5i51-1 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	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (2) #158 - Feb 2013 Proton-Gated Urea Channel similarity (2)

Deposited unit

A: Amidohydrolase

B: Amidohydrolase

hetero molecules

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

1

A: Amidohydrolase

B: Amidohydrolase

hetero molecules

A: Amidohydrolase

B: Amidohydrolase

hetero molecules

defined by author&software
Evidence: gel filtration
169 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	125.490, 208.050, 90.660
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-407- CL

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Protein , 2 types, 2 molecules AB

#1: Protein	Amidohydrolase Mass: 40127.410 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus wratislaviensis (bacteria) / Gene: Rhow_000804 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A402C2V4
#2: Protein	Amidohydrolase Mass: 42600.473 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus wratislaviensis (bacteria) / Gene: Rhow_000803 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A402C2Q3

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Non-polymers , 6 types, 87 molecules

#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO₄
#6: Chemical	ChemComp-FE / FE (III) ION Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#7: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N
Has protein modification	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: 3.8 Å³/Da / Density % sol: 67.8 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Tris/HCl (pH 8.5), 1 M ammonium sulfate and 12% (v/v) glycerol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.9791 Å
Detector	Type: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Jun 12, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9791 Å / Relative weight: 1
Reflection	Resolution: 2.75→45.12 Å / Num. obs: 59603 / % possible obs: 99.8 % / Redundancy: 5.79 % / B_iso Wilson estimate: 45.58 Å² / CC_1/2: 0.996 / R_merge(I) obs: 0.118 / R_rim(I) all: 0.13 / Net I/σ(I): 12.04
Reflection shell	Resolution: 2.75→2.91 Å / Redundancy: 5.93 % / R_merge(I) obs: 0.503 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 9588 / CC_1/2: 0.901 / R_rim(I) all: 0.551 / % possible all: 99.3

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Processing

Software

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

Refinement

Method to determine structure:

SAD / Resolution: 2.75→45.12 Å / SU ML: 0.3392 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.9078
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2503	1563	5 %
R_work	0.1896	29686	-
obs	0.1926	31249	99.87 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 56.5 Å²

Refinement step

Cycle: LAST / Resolution: 2.75→45.12 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5572	0	98	66	5736

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0094	5812
X-RAY DIFFRACTION	f_angle_d	1.0852	7924
X-RAY DIFFRACTION	f_chiral_restr	0.0559	839
X-RAY DIFFRACTION	f_plane_restr	0.0073	1034
X-RAY DIFFRACTION	f_dihedral_angle_d	28.4968	778

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 (%)
2.75-2.84	0.3616	138	0.2771	2630	X-RAY DIFFRACTION	98.68
2.84-2.94	0.3137	140	0.2446	2658	X-RAY DIFFRACTION	100
2.94-3.06	0.3097	140	0.232	2664	X-RAY DIFFRACTION	100
3.06-3.2	0.3006	142	0.2192	2682	X-RAY DIFFRACTION	100
3.2-3.36	0.2808	141	0.2058	2693	X-RAY DIFFRACTION	100
3.36-3.57	0.2409	141	0.2007	2666	X-RAY DIFFRACTION	100
3.57-3.85	0.2409	141	0.1796	2678	X-RAY DIFFRACTION	99.96
3.85-4.24	0.2292	142	0.1689	2706	X-RAY DIFFRACTION	100
4.24-4.85	0.2331	143	0.1477	2722	X-RAY DIFFRACTION	99.97
4.85-6.11	0.2273	145	0.1741	2741	X-RAY DIFFRACTION	100
6.11-45.12	0.2146	150	0.1858	2846	X-RAY DIFFRACTION	99.9

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	2.431353659	0.069157554875	-1.00135536355	1.49771925386	-0.233656414779	4.86707556749	0.0305882613838	-0.00598208120037	0.10482276155	0.0435243380745	0.201907503099	-0.0737025495242	-0.255701235886	0.0343928942396	-0.2232124305	0.241262276473	-0.109828968117	-0.0181463637395	0.329275538628	-0.02655447307	0.192466390536	27.7386989958	49.922694573	22.4916595843
2	0.300945240836	-1.01378265854	-0.705492822027	3.60542530305	2.07224813232	2.19095118114	-0.0917951023902	-0.75620282084	-0.0736674208188	0.921538672739	0.0500771424227	-0.0347449419268	0.428048341834	0.0165927703982	0.0254461603102	0.647193368928	-0.103522499086	-0.000322997659845	0.95518935685	0.0858456707336	0.309415523387	18.8437836216	43.8655018413	37.4042248864
3	3.50766259785	2.24846839294	2.36953635106	5.38223155915	1.19682988789	1.62777265964	0.0211011084045	0.0760858720926	-0.308191846862	-0.143553992451	0.219399112967	-0.456369236692	-0.0170901296393	0.453363912849	-0.207076841021	0.319436613628	-0.010387088249	0.0825161368266	0.479865247755	0.0341821281202	0.424215659468	33.3322827449	35.7251763032	23.2209117376
4	3.9556233751	0.373812732696	-1.99337840554	1.07639447208	-0.379097321188	2.29485748956	-0.0406846179094	-0.0953779792346	-0.0226617127478	-0.00024358168962	0.167512452347	-0.239841418855	-0.0607873381876	0.145571435117	-0.104466640597	0.371544740427	-0.144209143373	-0.0372258965752	0.335563694373	-0.00841686140329	0.202104400805	27.7507219152	46.8364115666	20.5556953347
5	2.01212047779	0.746054184508	0.332037323888	1.22053374094	0.333382926953	1.23465775552	-0.0117403426827	-0.225989979683	0.185917105388	0.10304491425	-0.107089419293	-0.00707907636804	-0.473670597229	0.295094160158	0.121209684997	0.400169730573	-0.119218874858	0.000220464020265	0.282732685831	0.00503016502771	0.141920507515	19.0382445125	53.3419594534	22.8178184804
6	1.57310365329	-0.0641239151138	0.113490293534	1.10562998259	0.175981814139	1.20809116561	-0.0544939564149	0.224474882839	-0.143227322151	-0.172707438625	0.02753240806	0.0878928881986	-0.198229070465	-0.0853495052351	0.032457344208	0.316317289279	-0.0283234027071	0.0136988940311	0.253353376842	-0.0394632008086	0.162783349641	10.6798322043	44.0328848731	12.1989807815
7	1.75478379764	-1.35822132861	0.292150843539	1.75602502986	0.269405618056	1.55599030711	0.118269494733	0.321738914979	-0.101249933809	-0.125395702932	-0.101036866922	0.0969325510038	-0.129566074542	-0.429957107434	0.0300613007533	0.509231266558	0.0331567704633	-0.025228059728	0.762581861799	-0.218985759755	0.247262184401	0.875809522468	43.3324410255	-2.79581242563
8	1.60146294859	0.197194772941	-0.489807660201	0.0981469368234	0.210390773461	1.15671344844	-0.029761018704	0.685310879983	-0.267440669412	-0.317801116373	-0.06144930858	-0.0136442084402	-0.279903044477	-0.175756885837	0.0765203984769	0.442726450564	-0.0776872634727	0.0556981949882	0.544106289481	-0.143070077816	0.27277889082	17.3509207476	44.4110601249	-1.25857171268
9	1.18636597041	-0.578124096314	-0.372970029303	2.19680948765	-0.357734422744	2.50854087912	0.0293192032299	0.514125845105	-0.00146328314717	-0.34747530577	0.0287463131454	-0.521593924908	-0.431728917278	0.314221992472	-0.0510001268236	0.41114980186	-0.18095356852	0.0817801146926	0.545594267967	-0.0512045461256	0.298070575868	30.2284319434	46.2283505119	2.65727878787
10	0.801407470992	0.62942884066	0.212131182226	2.04174358724	-0.161745800091	1.50353339709	0.175139597321	0.100251209937	-0.253490280039	0.0588051013301	-0.274703519681	0.369033627208	0.0578476779714	-0.317224185218	0.277207999014	0.664777970432	-0.108334032418	0.112391971798	1.00225706244	-0.648218664262	1.02172902431	-11.8951606982	14.7443124643	-6.2154599312
11	2.14654008898	0.403442319048	0.767981159393	3.08694876519	1.56058018051	0.9579115383	-0.155976176451	0.429737289708	-0.608415694755	-0.439081013177	0.131345648213	0.174971542487	0.0481116089441	-0.384650953484	0.0418026350925	0.422869137153	-0.031031670233	0.00293070149445	0.689514782234	-0.233585546956	0.671558988082	-20.7660941567	23.9053876543	12.9821894985
12	0.262332490432	-0.164136317636	0.525811840105	0.558075536214	0.0884676822346	1.42755394037	-0.0214200380896	0.112046534628	-0.0855483869411	-0.260413844582	-0.115962454741	0.346820878926	0.072167484271	-0.41287329328	0.257671325855	0.744267471979	-0.159179247537	-0.111727200116	1.12491871557	-0.63661866364	0.929665304784	-13.6234431995	18.9257572914	-13.3167745082
13	0.240299862084	0.156472048377	0.453164916894	1.30279286559	2.96066915991	6.84187561018	0.0187813741657	0.209553795666	-0.163493332778	-0.135122748698	-0.167831183842	0.24434945514	-0.278843418653	-0.243894556588	0.162002667655	0.460535211938	-0.0639511104332	0.0778357661192	0.58232247636	-0.434711973963	1.26358948324	-15.344926048	17.2208921207	9.01009856241
14	0.398107436357	-0.176809152574	-0.112256400411	0.495171060544	0.215308742304	0.459776065388	-0.203140990529	0.524092037263	-0.923149813579	-0.113918423535	-0.00726966510096	0.11824104198	0.108889878578	-0.138471882728	0.0683540048942	0.444699589817	-0.0844340853152	0.141101225202	0.400088856228	-0.416087147961	0.959942680448	4.45426510492	21.0528030972	5.21344752386
15	0.160603895314	-0.00797525640514	-0.141585216141	0.444199459136	0.198169689939	0.723378774964	0.0234287353263	0.135702570975	-0.109017660364	-0.307688466927	-0.0761660996136	0.0464437824151	-0.13163806833	-0.022610586628	-0.0360500122451	0.635860712321	-0.0593067221751	0.120041512472	1.09467429563	-0.781604253813	0.970853159912	1.33241731926	22.0931977176	-12.0432168514

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 27 through 52 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 53 through 71 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 72 through 95 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 96 through 127 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 128 through 193 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 194 through 274 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 275 through 291 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 292 through 339 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 340 through 380 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 10 through 35 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 36 through 86 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 87 through 105 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 106 through 141 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 142 through 328 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 329 through 375 )

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-Non-polymers , 6 types, 87 molecules

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+About Yorodumi

-News

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

-Aug 12, 2020. Covid-19 info

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Protein , 2 types, 2 molecules AB

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Experimental details

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