PDB-8il5: Crystal structure of alcohol oxidase PcAOX(M59V/Q60P/R61N)(Phaner...

ID or keywords:

Entry

Database: PDB / ID: 8il5

Title

Crystal structure of alcohol oxidase PcAOX(M59V/Q60P/R61N)(Phanerochaete chrysosporium)

Components

Alcohol oxidase

Keywords

OXIDOREDUCTASE

Function / homology

Function and homology information

alcohol oxidase / oxidoreductase activity, acting on CH-OH group of donors / flavin adenine dinucleotide binding
Similarity search - Function

Biological species

Phanerodontia chrysosporium (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.50006027028 Å

Authors

Wu, B. / Wang, Y.

Funding support

1items

Citation

Journal: To Be Published
Title: Crystal structure of alcohol oxidase PcAOX(M59V/Q60P/R61N)(Phanerochaete chrysosporium)
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	8il5.cif.gz	590.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8il5.ent.gz	405.2 KB	Display	PDB format
PDBx/mmJSON format	8il5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8il5_validation.pdf.gz	1.8 MB	Display	wwPDB validaton report
Full document	8il5_full_validation.pdf.gz	1.8 MB	Display
Data in XML	8il5_validation.xml.gz	45.2 KB	Display
Data in CIF	8il5_validation.cif.gz	61.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/il/8il5 ftp://data.pdbj.org/pub/pdb/validation_reports/il/8il5	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: Alcohol oxidase

B: Alcohol oxidase

hetero molecules

149 kDa, 2 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)	161.26, 161.26, 113.34
Angle α, β, γ (deg.)	90.0, 90.0, 90.0
Int Tables number	90
Space group name H-M	P42₁2
Space group name Hall	P4ab2ab
Symmetry operation	#1: x,y,z #2: -y+1/2,x+1/2,z #3: y+1/2,-x+1/2,z #4: x+1/2,-y+1/2,-z #5: -x+1/2,y+1/2,-z #6: -x,-y,z #7: y,x,-z #8: -y,-x,-z

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	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	GLU	GLU	ASN	ASN	chain 'A'	A	A	5 - 43	9 - 47
1	2	ASP	ASP	GLN	GLN	chain 'A'	A	A	46 - 136	50 - 140
1	3	ASP	ASP	ASN	ASN	chain 'A'	A	A	142 - 154	146 - 158
1	4	GLN	GLN	SER	SER	chain 'A'	A	A	157 - 248	161 - 252
1	5	HIS	HIS	VAL	VAL	chain 'A'	A	A	258 - 336	262 - 340
1	6	SER	SER	PRO	PRO	chain 'A'	A	A	358 - 631	362 - 635
1	7	HIS	HIS	PRO	PRO	chain 'A'	A	A	637 - 641	641 - 645
2	8	GLU	GLU	ASN	ASN	chain 'B'	B	B	5 - 43	9 - 47
2	9	ASP	ASP	GLN	GLN	chain 'B'	B	B	46 - 136	50 - 140
2	10	ASP	ASP	ASN	ASN	chain 'B'	B	B	142 - 154	146 - 158
2	11	GLN	GLN	SER	SER	chain 'B'	B	B	157 - 248	161 - 252
2	12	HIS	HIS	VAL	VAL	chain 'B'	B	B	258 - 336	262 - 340
2	13	SER	SER	PRO	PRO	chain 'B'	B	B	358 - 636	362 - 640

#1: Protein	Alcohol oxidase Mass: 73321.594 Da / Num. of mol.: 2 / Mutation: M59V, Q60P, R61N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Phanerodontia chrysosporium (fungus) / Gene: AOX / Production host: Escherichia coli (E. coli) / References: UniProt: A0A977TIR6, alcohol oxidase
#2: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: SO₄ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 77 / 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: 51.44 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, hanging drop Details: 1.6 M ammonium sulfate, 0.1M MES pH 6.5, 10% (v/v) 1,4-Dioxane

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9769 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 2, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9769 Å / Relative weight: 1
Reflection	Resolution: 2.46→24.01 Å / Num. obs: 54647 / % possible obs: 99.9 % / Redundancy: 51 % / CC_1/2: 0.998 / Net I/σ(I): 14.9
Reflection shell	Resolution: 2.46→2.52 Å / Num. unique obs: 3996 / CC_1/2: 0.72

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.50006027028→23.181962923 Å / SU ML: 0.285919731352 / Cross valid method: FREE R-VALUE / σ(F): 1.34751449172 / Phase error: 23.02007787

	R_factor	Num. reflection	% reflection
R_free	0.213396744737	2579	4.95532712076 %
R_work	0.165963746622	49466	-
obs	0.168335889111	52045	99.9500681761 %

Solvent computation

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

Displacement parameters

B_iso mean: 65.7646710666 Å²

Refinement step

Cycle: LAST / Resolution: 2.50006027028→23.181962923 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9648	0	95	77	9820

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.00883373293254	10001
X-RAY DIFFRACTION	f_angle_d	1.30866879468	13605
X-RAY DIFFRACTION	f_chiral_restr	0.0595381218024	1464
X-RAY DIFFRACTION	f_plane_restr	0.00755485533364	1776
X-RAY DIFFRACTION	f_dihedral_angle_d	16.219154517	3663

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 (%)
2.5001-2.5481	0.324015074094	153	0.251160671591	2675	X-RAY DIFFRACTION	99.9646518204
2.5481-2.6	0.328570824638	133	0.242724698759	2732	X-RAY DIFFRACTION	99.9651081647
2.6-2.6565	0.328021295895	144	0.235241277504	2693	X-RAY DIFFRACTION	99.8943661972
2.6565-2.7182	0.249814682521	137	0.221457905865	2701	X-RAY DIFFRACTION	100
2.7182-2.7861	0.242043766292	133	0.220294826567	2728	X-RAY DIFFRACTION	99.9301432064
2.7861-2.8613	0.274476514139	132	0.222167264762	2731	X-RAY DIFFRACTION	100
2.8613-2.9453	0.30530618221	141	0.224075299795	2704	X-RAY DIFFRACTION	100
2.9453-3.0402	0.269665122259	149	0.209092627042	2723	X-RAY DIFFRACTION	100
3.0402-3.1486	0.247013662629	150	0.198688509896	2725	X-RAY DIFFRACTION	100
3.1486-3.2743	0.256587138042	148	0.197793209994	2713	X-RAY DIFFRACTION	100
3.2743-3.4229	0.215643730721	137	0.181347716468	2738	X-RAY DIFFRACTION	100
3.4229-3.6027	0.217853510198	150	0.168085262254	2734	X-RAY DIFFRACTION	99.9653379549
3.6027-3.8275	0.201000017863	151	0.153615936173	2733	X-RAY DIFFRACTION	99.9653379549
3.8275-4.1215	0.188838960656	141	0.138836812429	2772	X-RAY DIFFRACTION	99.9656829101
4.1215-4.5335	0.167032291316	127	0.126581227685	2793	X-RAY DIFFRACTION	100
4.5335-5.1831	0.177093123535	151	0.131923611634	2798	X-RAY DIFFRACTION	100
5.1831-6.5061	0.197615742258	138	0.160221943343	2824	X-RAY DIFFRACTION	99.8988195616
6.5061-23.18	0.18250963291	164	0.145149368513	2949	X-RAY DIFFRACTION	99.5841330774

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	1.34300992181	-0.352716241936	-0.0777303089742	0.816416473242	0.335723391431	1.99466013979	-0.0112594702441	-0.0106206609576	-0.240823513381	-0.0366778940116	-0.00796980045071	0.259814475005	0.365719438409	-0.173146600758	0.0300241788628	0.45820199728	-0.0430035760481	-0.0284813778899	0.433047267763	-0.0663957995411	0.462689571725	-73.6977000168	-34.75111098	-23.4444167855
2	0.747131784989	0.243792897716	0.173998600854	0.492135534576	0.114868341701	0.635984669774	-0.00553265627704	0.0314124880527	0.0421716689209	-0.0139716608284	0.00992138166559	-0.0132991964983	0.058856478665	0.0718488412033	-0.0068642706631	0.345444000027	0.0152214761915	-0.0021284137891	0.347332912073	-0.0309571278318	0.3815941227	-54.810410274	-18.4675125313	-14.6868888291
3	0.74354445553	0.156456117859	0.318481143544	0.484809532696	0.0743665426189	0.83326480804	-0.0375754401076	0.0877741260587	-0.14900153837	-0.0360452255986	0.0721285610402	0.0320900529145	0.18782933433	0.00558063746242	-0.0383318928592	0.36697105297	0.01391481685	0.0156196797976	0.33177995955	-0.0365136440965	0.363644683995	-64.4233972673	-36.5143876978	-16.7022256081
4	0.503359050467	0.043514762319	0.136089681615	0.91799669511	-0.0081854229069	0.604414420035	-0.0123244593486	-0.0255014409105	0.0413926811215	0.0742257834973	0.0391522380957	-0.126108623514	0.0500322836408	0.0399575965496	-0.021065605039	0.334719003908	0.0279911540047	-0.00301653209351	0.345243140848	-0.0297000222542	0.358955116958	-49.1676591171	-18.630717967	-5.44188425829
5	0.993708879404	-0.517625565217	0.0594813827396	1.02152045841	0.371024690842	0.50270865797	0.0711963236378	-0.155009317066	0.246363053642	0.33091412745	-0.0242761574432	-0.154463782222	-0.243677936111	0.0695369838875	-0.0109018392708	0.516146248127	0.0113989111332	-0.0158238323291	0.390810148647	-0.0476550412656	0.445902687707	-43.6754375049	-5.63727961102	12.6308905078
6	0.847785211588	-0.105427173422	0.410146462754	0.909711843448	0.896024691163	1.70509116527	-0.00791920734808	0.0285822945324	-0.0605430833378	0.0875480745157	-0.100444509333	0.0874107816916	0.20744806264	-0.0183732569628	0.142212094062	0.404771374323	0.0134962188515	0.0125685448877	0.356906363737	-0.0399176061254	0.422623609973	-47.4052103441	-33.4329764944	-13.3217744892
7	1.12167293925	0.210051018012	0.141048795213	0.823062803346	-0.0842837469008	1.27695858815	-0.0502075348049	0.0571131999765	0.0670400270685	-0.00293000081959	0.00194356390281	-0.0961750181142	-0.119374294508	-0.021534098425	0.0277741696979	0.452525300668	0.0196159181372	0.0128458243903	0.3928497461	-0.0127234411862	0.416481220149	-61.0181745912	-26.2822657981	-27.2382178401
8	1.65981650553	0.295546222821	0.177809329864	0.768013181518	0.537644833083	0.739173965018	0.208039590185	-0.406782712727	0.539167893307	0.0876436501967	-0.0671211242574	-0.0505837324075	-0.00744256601974	0.043024182477	-0.101735878037	0.949713139948	-0.00858933487206	0.0573109207085	0.851011699015	-0.182534463888	0.76937375936	-41.9477405825	-3.25749554447	48.1810174621
9	1.3038600397	0.368591394274	0.418062228511	0.743814950291	0.697829263776	1.49389128648	0.11662714522	-0.280922418334	0.232089007529	0.255114273253	-0.000997078193816	-0.0631661305726	0.0434632944735	0.0892170559978	-0.130563444654	0.594531385473	0.038850970378	0.0558492060758	0.50994174323	-0.0743414620787	0.47469182791	-43.0781244194	-12.8652828833	40.5530055333

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -3 through 46 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 47 through 191 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 192 through 322 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 323 through 474 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 475 through 541 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 542 through 588 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 589 through 641 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 5 through 135 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 136 through 636 )

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