PDB-8il4: Crystal structure of alcohol oxidase ParAOX(M59V/Q60P/R61N/F101S/...

ID or keywords:

Entry

Database: PDB / ID: 8il4

Title

Crystal structure of alcohol oxidase ParAOX(M59V/Q60P/R61N/F101S/N602H)(Polyporus arcularius)

Components

GMC oxidoreductase

Keywords

OXIDOREDUCTASE /

alcohol oxidase

Function / homology

Function and homology information

flavin-dependent halogenase activity / oxidoreductase activity, acting on CH-OH group of donors /

flavin adenine dinucleotide binding
Similarity search - Function

Biological species

Polyporus arcularius HHB13444 (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.35500070154 Å

Authors

Wu, B. / Wang, Y.

Funding support

1items

Citation

Journal: To Be Published
Title: Crystal structure of alcohol oxidase ParAOX(M59V/Q60P/R61N/F101S/N602H)(Polyporus arcularius)
Authors: Wu, B. / Wang, Y.

History

Deposition	Mar 1, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Mar 6, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8il4.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb8il4.ent.gz	771.7 KB	Display	PDB format
PDBx/mmJSON format	8il4.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/il/8il4 ftp://data.pdbj.org/pub/pdb/validation_reports/il/8il4	HTTPS FTP

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Related structure data

Similar structure data	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	#77 - May 2006 Glucose Oxidase similarity (7)

Deposited unit

A: GMC oxidoreductase

B: GMC oxidoreductase

C: GMC oxidoreductase

D: GMC oxidoreductase

hetero molecules

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

1

A: GMC oxidoreductase

hetero molecules

C: GMC oxidoreductase

hetero molecules

defined by author&software
Evidence: gel filtration
146 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: GMC oxidoreductase

hetero molecules

D: GMC oxidoreductase

hetero molecules

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

Unit cell

Length a, b, c (Å)	71.706, 187.433, 118.532
Angle α, β, γ (deg.)	90.0, 90.294, 90.0
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
3	1
4	1

NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	PRO	PRO	ARG	ARG	chain 'A'	A	A	4 - 44	4 - 44
1	2	ASP	ASP	ASN	ASN	chain 'A'	A	A	66 - 154	66 - 154
1	3	GLN	GLN	ARG	ARG	chain 'A'	A	A	157 - 332	157 - 332
1	4	LYS	LYS	LEU	LEU	chain 'A'	A	A	335 - 341	335 - 341
1	5	SER	SER	TYR	TYR	chain 'A'	A	A	356 - 507	356 - 507
1	6	ARG	ARG	HIS	HIS	chain 'A'	A	A	522 - 635	522 - 635
2	7	PRO	PRO	ARG	ARG	chain 'B'	B	B	4 - 44	4 - 44
2	8	ASP	ASP	ASN	ASN	chain 'B'	B	B	66 - 154	66 - 154
2	9	GLN	GLN	ARG	ARG	chain 'B'	B	B	157 - 332	157 - 332
2	10	LYS	LYS	LEU	LEU	chain 'B'	B	B	335 - 341	335 - 341
2	11	SER	SER	TYR	TYR	chain 'B'	B	B	356 - 507	356 - 507
2	12	ARG	ARG	HIS	HIS	chain 'B'	B	B	522 - 635	522 - 635
3	13	PRO	PRO	ARG	ARG	chain 'C'	C	C	4 - 44	4 - 44
3	14	ASP	ASP	ASN	ASN	chain 'C'	C	C	66 - 154	66 - 154
3	15	GLN	GLN	ARG	ARG	chain 'C'	C	C	157 - 332	157 - 332
3	16	LYS	LYS	LEU	LEU	chain 'C'	C	C	335 - 341	335 - 341
3	17	SER	SER	TYR	TYR	chain 'C'	C	C	356 - 507	356 - 507
3	18	ARG	ARG	HIS	HIS	chain 'C'	C	C	522 - 635	522 - 635
4	19	PRO	PRO	ARG	ARG	chain 'D'	D	D	4 - 44	4 - 44
4	20	ASP	ASP	ASN	ASN	chain 'D'	D	D	66 - 154	66 - 154
4	21	GLN	GLN	ARG	ARG	chain 'D'	D	D	157 - 332	157 - 332
4	22	LYS	LYS	LEU	LEU	chain 'D'	D	D	335 - 341	335 - 341
4	23	SER	SER	TYR	TYR	chain 'D'	D	D	356 - 507	356 - 507
4	24	ARG	ARG	HIS	HIS	chain 'D'	D	D	522 - 635	522 - 635

#1: Protein	GMC oxidoreductase Mass: 72075.961 Da / Num. of mol.: 4 / Mutation: M59V, Q60P, R61N, F101S, N602H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Polyporus arcularius HHB13444 (fungus) / Strain: HHB13444 / Gene: K466DRAFT_604656 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5C3NW19
#2: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
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: 2.82 Å³/Da / Density % sol: 56.32 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, hanging drop Details: 200 mM Sodium chloride, 100 mM HEPES pH 7.5, 30% PEG 400

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9796 Å
Detector	Type: RDI CMOS_8M / Detector: CMOS / Date: Oct 2, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9796 Å / Relative weight: 1
Reflection	Resolution: 3.35→50 Å / Num. obs: 42191 / % possible obs: 94.1 % / Redundancy: 4.6 % / B_iso Wilson estimate: 53.4137523476 Å² / CC_1/2: 0.977 / Net I/σ(I): 7.5
Reflection shell	Resolution: 3.35→3.54 Å / Num. unique obs: 5598 / CC_1/2: 0.761

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692+SVN	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing
autoPROC		data processing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.35500070154→45.5669687023 Å / SU ML: 0.36080228305 / Cross valid method: FREE R-VALUE / σ(F): 1.33786346252 / Phase error: 24.2265251247

	R_factor	Num. reflection	% reflection
R_free	0.243177306119	1996	4.74075481557 %
R_work	0.193748106925	40107	-
obs	0.196133617571	42103	94.0617948661 %

Solvent computation

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

Displacement parameters

B_iso mean: 43.3968550908 Å²

Refinement step

Cycle: LAST / Resolution: 3.35500070154→45.5669687023 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18812	0	212	0	19024

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0141529710757	19490
X-RAY DIFFRACTION	f_angle_d	1.3264287706	26545
X-RAY DIFFRACTION	f_chiral_restr	0.0675593516804	2894
X-RAY DIFFRACTION	f_plane_restr	0.00669104922336	3467
X-RAY DIFFRACTION	f_dihedral_angle_d	15.4041523784	7014

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 (%)
3.355001-3.4389	0.350081503986	122	0.274977828204	2400	X-RAY DIFFRACTION	95.747911921
3.4389-3.5318	0.315175635672	138	0.250561701304	2786	X-RAY DIFFRACTION	99.1522550017
3.5318-3.6357	0.279373450843	155	0.238107779512	3034	X-RAY DIFFRACTION	99.65625
3.6357-3.753	0.255701482946	101	0.230276385706	2050	X-RAY DIFFRACTION	67.535321821
3.753-3.8871	0.279308068738	135	0.221115361536	2829	X-RAY DIFFRACTION	96.0777957861
3.8871-4.0426	0.217171333783	131	0.18934065139	2652	X-RAY DIFFRACTION	99.641962048
4.0426-4.2265	0.229160947197	152	0.18682885533	3076	X-RAY DIFFRACTION	99.9690306596
4.2265-4.4491	0.22753678255	146	0.173689409843	3020	X-RAY DIFFRACTION	99.9368686869
4.4491-4.7276	0.217919991237	151	0.173076208152	3027	X-RAY DIFFRACTION	99.9056900346
4.7276-5.0922	0.204391627176	155	0.168929558738	3053	X-RAY DIFFRACTION	99.937694704
5.0922-5.6038	0.246724219263	150	0.189265216608	3036	X-RAY DIFFRACTION	99.8120300752
5.6038-6.4128	0.305563724732	147	0.202564847467	3035	X-RAY DIFFRACTION	99.7492163009
6.4128-8.0721	0.229227244947	156	0.181855185994	3065	X-RAY DIFFRACTION	99.7831474597
8.0721-45.5	0.202532111158	157	0.158019533531	3044	X-RAY DIFFRACTION	98.4317343173

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	0.977369826129	0.275582160371	-0.13944529106	1.92633373198	-0.175543193851	1.38837119947	-0.00648404591083	0.0513442779597	-0.122750416258	-0.168278214981	-0.0358987711325	0.051350298509	0.179362278013	-0.0165771367035	0.0645783693381	0.295623796463	-0.0405382306485	-0.0363767860057	0.335095052794	-0.00715662872612	0.336331014409	21.1580561699	34.3558911746	15.5623826672
2	0.60958523136	0.0734541422296	-0.524936026069	1.47426353981	-0.913228508392	1.73723538024	-0.153905522106	0.0278379524301	-0.0893926282649	-0.185333189231	0.0486286412308	0.0738788363291	0.506665388487	0.123038849733	0.0860600369129	0.210994347499	-0.00985285955022	-0.0634476312205	0.306210247231	-0.00986524465761	0.379689002409	17.7502409322	33.1421331902	14.0912831712
3	0.557078607177	-0.451358814256	-0.415758100642	1.00644959164	-0.531464780246	2.51429748414	0.0995891501336	0.0377762911409	-0.0364812984211	-0.232798368768	-0.048865741584	-0.0633332770551	0.196240715629	0.0912773989842	-0.0610473566938	0.249109795887	-0.0180421075772	-0.0337791533887	0.288274034637	-0.0151794994157	0.377637534221	20.9591774392	49.0065276946	5.02380227756
4	3.37408503552	1.35989369605	0.665978855958	0.342071996481	0.250731901378	0.323478801025	0.110097500854	0.383371921133	-0.00776646232835	-0.21521811283	-0.00449048962582	0.00899924676276	-0.202330590898	-0.043707909529	-0.021830949726	0.638703469197	0.0141754449455	0.0250558767798	0.516895420395	-0.0237563765894	0.532453450052	14.2733734947	60.5924392393	-19.6808189693
5	0.7070458295	-0.308121184525	0.0474995460179	1.8942235807	-0.342719855434	1.47885791923	-0.0526580197839	0.00620809082162	-0.0350517636508	0.0190515616936	-0.0351637365027	-0.211766716984	0.154837430097	0.0330060206101	0.0819857373161	0.207018098659	-0.00504837648583	0.0268800872655	0.410637186221	0.000847196648062	0.337271841361	26.2354218629	38.8715079057	17.405410078
6	1.61849908954	-0.333254252891	1.36412777096	3.62529485221	1.25090767602	2.13139150076	0.309907515468	-0.147834312908	0.109632067366	0.184685872662	-0.190800268756	0.770242822665	-0.510338763561	-0.787680134525	-0.0312682003778	0.201319849372	0.108722806437	-0.0423631611808	0.632109910255	-0.0284011737244	0.568021929787	-23.5372366168	68.6469802535	41.3100467315
7	0.929024637589	0.245715465611	0.0854651096754	0.828875103015	-0.370222862544	1.36433419549	0.0116283347429	-0.0414376514544	0.212023164952	0.144936255934	-0.0313571003283	-0.00281807916705	-0.192592943743	-0.0735504492668	0.0268169529923	0.195467713214	0.0119786679167	-0.0463862343247	0.389878483049	-0.025509132896	0.469426038042	-15.6842927609	62.1267047874	50.1766172183
8	1.66863382624	0.285038392943	-0.402844425349	0.32987416043	-0.0765676323805	2.49283221811	0.000323939726797	-0.226676564725	0.146722758272	0.206382556596	-0.00453502962321	-0.106444354043	0.0310232629724	0.0887060044717	0.00269282811055	0.316003187429	-0.00321854994377	-0.0211621459821	0.368442001426	-0.0449974617516	0.378926887928	-13.7202627358	49.4279410893	63.9681223366
9	2.76631603717	-0.164187867007	-0.731798135202	0.722577607091	-0.273403232975	1.47570260964	0.074152471611	-0.660530857244	0.152834175102	0.673245800926	0.00792375844564	-0.269731769406	0.395192027183	0.458010750341	-0.116884383834	0.623239144414	-0.1456916963	-0.0372095663041	0.517279151347	-0.00676441413799	0.496989069141	-15.6619978018	40.4534112618	76.7915535622
10	2.12235778953	0.384696860694	-0.355889335468	2.04594460596	-0.350041595063	2.08528646575	-0.11752887632	0.249919898528	0.237503526477	0.0161863347351	0.157591558603	-0.099692597476	-0.208338491204	-0.139331557593	-0.0162472454837	0.23488542085	-0.0298817677559	-0.0919574459268	0.330633696004	-0.0251100084366	0.377414096302	-8.89486466216	65.5247223288	42.5576836583
11	3.82720685382	0.0392579872664	-0.483559758238	0.554928353787	-0.97091341422	1.82101680426	-0.224060177835	-0.338578459296	-0.287260563786	0.286776496566	0.286760270574	-0.00188885554025	0.261862965957	-0.167766909353	-0.113107479141	0.520132213253	0.0166342911733	-0.0272543177458	0.358321451309	0.126394223435	0.510008952485	4.91710479092	-11.2966986648	41.6779615838
12	0.162344348914	0.208187688254	0.704924733903	0.989495059008	0.631858204213	1.53365110989	-0.146432395927	0.0223790727733	-0.0437149063987	-0.244804892204	0.175906766259	-0.423605297986	0.0322329812269	0.282439782544	0.0377208331899	0.518884271135	-0.0262837258666	0.0470136072607	0.44591695041	0.0102354689858	0.53279590125	11.0379734683	-8.16390181915	21.9754267504
13	2.81314070613	-0.503515452868	0.273259544528	1.7388022234	0.0373264219014	1.5930196567	-0.0144854804693	-0.318729716455	-0.191085394418	0.339157737407	0.170882735143	0.271724685865	0.164778264684	-0.158597523921	-0.0306033198178	0.559403061273	-0.00948074173693	-0.00748650692007	0.457108291863	0.0188804490393	0.324018827093	-6.74229349345	-4.2720693344	46.036752845
14	0.999953768869	0.00509747053343	-0.358076260197	1.84742206657	0.361364088744	1.99230063922	-0.0175821436723	-0.00425723449871	0.0142172530707	-0.127775778082	0.129204616533	-0.0412678958312	-0.16440296667	0.110860078527	-0.125874002553	0.357713839278	-0.0562455710687	-0.0275099084013	0.335803123028	-0.041643329557	0.426205468127	-1.09317803285	-13.0747454078	13.5403183296
15	0.704300424224	-1.2589721829	0.127328906927	1.98368481148	-0.0527750048981	0.0892317949163	0.108859423699	0.543221835785	-0.353990903954	-0.732966815026	-0.190364361328	-0.246059123846	-0.0214836355731	0.189908597986	0.0541594986488	0.575514409339	-0.0725030493074	-6.92853973248E-5	0.688991945547	-0.10175239664	0.488454167253	-0.741120270104	-29.5828833268	-3.04618831502
16	0.615526354283	0.697063208926	-0.257611008825	1.58685798217	0.396301411879	1.70213828814	-0.116904373901	0.0284788503749	0.196204974437	-0.103758372086	-0.0228336930038	0.32591970845	-0.121142457364	-0.256008725398	0.225437411933	0.395389237679	0.0619633681679	-0.0880407186916	0.400667950347	-0.0161972175739	0.455376650075	-6.66637110604	-2.71434608876	23.0139707631
17	2.54770741975	0.327325395221	0.960982711015	2.51561525229	-0.362389537963	3.19519183105	-0.497433144846	0.190082512017	-0.186735536533	0.17322949344	0.186281212004	-0.368930048591	-0.270663179733	0.481840794323	0.284790704091	0.416729783656	0.000554390033245	0.0206155051654	0.384460154612	0.0295188233626	0.418466315951	11.867143663	-1.20122037814	34.485947982
18	0.707280210971	0.716460027385	-0.820586580453	1.63383357177	-0.38461767366	1.44365404127	-0.304030952992	0.0991768187877	-0.0869355189043	0.0895353959426	0.0632819943046	0.278307113831	0.360890785746	-0.0786497882971	0.219740425489	0.784119894883	-0.0536635701939	0.17912670776	0.496478791973	-0.0745461127259	0.605505635989	29.1053654538	13.1480017402	95.8099942393
19	0.952006768528	0.458947988283	-0.332388721233	1.05461174178	-0.204544392398	1.21397518515	-0.533261093605	0.168918664825	-0.0579751327898	0.058559327126	0.372952624719	0.110441942343	0.492204964453	-1.19507862662	0.112001112934	0.903695304266	-0.180599234043	0.00764213823582	0.655413833967	-0.0960906758962	0.655987734586	19.4695322994	19.1071813458	77.8570431626
20	0.98853510161	0.195470116452	-0.284065418075	0.305331027549	-0.186014120586	2.32713690397	-0.312389772346	-0.172941310605	-0.221546034702	0.212158257436	0.0580314883058	-0.11521464697	0.262207221045	0.0704030284895	0.252875369789	0.684656236482	0.0465499978322	0.130663095161	0.453911535233	-0.0206239223349	0.583527829478	38.9093450649	14.3891255893	102.700480755
21	2.34585463035	1.51398783399	0.846708356671	2.06542306673	-0.560366728247	1.23684630082	-0.280194282003	0.0902488051321	0.262513208127	0.189108582104	0.082735573515	1.00378605167	0.270493371992	-0.713677901706	0.118590607125	0.68690346273	-0.0775619552167	-0.000171676780711	0.659509610816	0.142282567921	0.605033958645	26.1940775975	27.4979159056	78.0623550374
22	1.16826812638	-0.102411984546	-0.367456673522	1.43300737561	0.420668811646	0.637358340962	-0.118077313546	0.168251158555	-0.0200293841768	-0.221794883931	-0.0131080470336	0.133658130306	0.528533476465	-0.30911029955	0.0867334644833	0.698739107045	-0.195993242142	0.0789156923664	0.51327692579	-0.0287120423801	0.473513075021	38.6211694777	24.2666016905	71.1364687153
23	0.820089851118	0.376022808245	-0.46471158094	1.41048271887	-0.212612239179	1.64263436828	-0.30524517444	0.0141276728981	-0.243002616198	-0.121525547679	0.180418955303	-0.0124008764771	0.521818427334	0.0649956856593	0.193643296768	0.81800190343	-0.0341866290581	0.179729074433	0.456997817122	-0.00871645098968	0.525829090259	33.4141711566	8.45848563078	92.8586006324

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 149 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 150 through 268 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 269 through 488 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 489 through 539 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 540 through 637 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 4 through 72 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 73 through 334 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 335 through 499 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 500 through 553 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 554 through 635 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 4 through 72 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 73 through 215 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 216 through 302 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 303 through 472 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 473 through 539 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 540 through 586 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 587 through 643 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 3 through 149 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 150 through 205 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 206 through 327 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 328 through 375 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 376 through 539 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 540 through 638 )

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