PDB-3bly: Pyranose 2-oxidase from Trametes multicolor, E542K/L537W

ID or keywords:

Entry

Database: PDB / ID: 3bly

Title

Pyranose 2-oxidase from Trametes multicolor, E542K/L537W

Components

Pyranose oxidase

Keywords

OXIDOREDUCTASE / GMC OXIDOREDUCTASE / E542K/L537W THERMOSTABLE MUTANT /

ROSSMANN FOLD / PHBH FOLD /

HOMOTETRAMER / 8-ALPHA-(N3) HISTIDYL FLAVINYLATION

Function / homology

Function and homology information

pyranose oxidase /

pyranose oxidase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen /

flavin adenine dinucleotide binding /

periplasmic space
Similarity search - Function

Biological species

Trametes multicolor (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 1.9 Å

Authors

Tan, T.C. / Divne, C.

Citation

Journal: Febs J. / Year: 2009
Title: Improving thermostability and catalytic activity of pyranose 2-oxidase from Trametes multicolor by rational and semi-rational design
Authors: Spadiut, O. / Leitner, C. / Salaheddin, C. / Varga, B. / Vertessy, B.G. / Tan, T.C. / Divne, C. / Haltrich, D.

History

Deposition	Dec 11, 2007	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Dec 2, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Nov 12, 2014	Group: Structure summary
Revision 1.3	Nov 10, 2021	Group: Database references / Derived calculations Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3bly.cif.gz	133.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3bly.ent.gz	110.1 KB	Display	PDB format
PDBx/mmJSON format	3bly.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bl/3bly ftp://data.pdbj.org/pub/pdb/validation_reports/bl/3bly	HTTPS FTP

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Related structure data

Related structure data	3bg6C 3bg7C 1tt0 2igk 2igm 2ign 2igo C: citing same article (ref.)
Similar structure data	4mos-1 2f6c-1 3pl8-1 4moh-1 4moq-1 2f5v-1 4mol-d 3lsm-1 4mog-1 4mof-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	#77 - May 2006 Glucose Oxidase similarity (2)

Deposited unit

A: Pyranose oxidase

hetero molecules

70.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Pyranose oxidase

hetero molecules

A: Pyranose oxidase

hetero molecules

A: Pyranose oxidase

hetero molecules

A: Pyranose oxidase

hetero molecules

defined by author&software
282 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	103.430, 103.430, 118.560
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	94
Space group name H-M	P4₂2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-1122- HOH

#1: Protein	Pyranose oxidase / / Pyranose 2-oxidase Mass: 69486.906 Da / Num. of mol.: 1 / Mutation: E542K, L537W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trametes multicolor (fungus) / Gene: p2o / Plasmid: pET21(d+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7ZA32, pyranose oxidase
#2: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Comment: FAD*YM
#3: Chemical	ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer) Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₃NO₄S / Comment: pH buffer*YM
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 354 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.28 Å³/Da / Density % sol: 46.09 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: 12-14(w/v)% monomethylether PEG 2000, 0.1M Mes, 50mM MgCl2, 25% glycerol, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 7, 2007 / Details: mirrors
Radiation	Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.931 Å / Relative weight: 1
Reflection	Resolution: 1.9→51 Å / Num. all: 51240 / Num. obs: 51240 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.6 % / R_sym value: 0.121 / Net I/σ(I): 17.2
Reflection shell	Resolution: 1.9→2 Å / Redundancy: 12.7 % / Mean I/σ(I) obs: 4.8 / Num. unique all: 7193 / R_sym value: 0.627 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
ADSC	Quantum	data collection
XDS		data reduction
XSCALE		data scaling
REFMAC		phasing

Refinement

Method to determine structure:

FOURIER SYNTHESIS / Resolution: 1.9→47.4 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.951 / SU B: 4.42 / SU ML: 0.068 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.113 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.18124	504	1 %	RANDOM
R_work	0.14864	-	-	-
all	0.14897	50735	-	-
obs	0.14897	50735	99.96 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 11.174 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.31 Å²	0 Å²	0 Å²
2-	-	-0.31 Å²	0 Å²
3-	-	-	0.63 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→47.4 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4524	0	65	354	4943

Refine LS restraints

Refine-ID	Type	Dev ideal
X-RAY DIFFRACTION	r_bond_refined_d	0.022
X-RAY DIFFRACTION	r_bond_other_d	0.002
X-RAY DIFFRACTION	r_angle_refined_deg	1.911
X-RAY DIFFRACTION	r_angle_other_deg	0.983
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.605
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.413
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.717
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.58
X-RAY DIFFRACTION	r_chiral_restr

LS refinement shell

Resolution: 1.9→2.003 Å / Total num. of bins used: 10

	R_factor	Num. reflection	% reflection
R_free	0.205	67	-
R_work	0.152	7301	-
obs	-	-	99.97 %

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	1.4791	0.2965	-0.2289	1.6695	-0.0869	1.4465	-0.0003	0.1253	0.0026	-0.0668	0.0124	0.0305	-0.0172	-0.07	-0.0121	0.0573	-0.0046	0.0023	0.0795	-0.0076	0.0448	68.6426	51.0744	17.207
2	1.051	0.0768	-0.0251	0.2395	-0.6836	1.988	0.0175	-0.1802	0.1256	0.1265	-0.0155	0.2079	-0.1923	-0.2701	-0.002	0.0442	-0.0116	0.0034	0.0815	-0.0097	0.0696	52.1675	59.9679	33.0099
3	1.016	0.4805	-0.339	0.5136	-0.2274	0.1288	0.0148	-0.0443	-0.0237	0.0011	-0.0038	-0.0312	-0.036	0.0031	-0.011	0.0574	-0.0041	0.0054	0.0734	-0.0093	0.0451	60.421	35.2746	51.4149
4	0.5198	-0.5665	1.1635	1.2379	-2.0655	4.5449	-0.0279	-0.0433	0.0198	0.1037	-0.0234	-0.0622	-0.0367	0.1029	0.0513	0.0716	0.0035	0.0184	0.0833	-0.0136	0.06	68.2333	47.3385	40.038
5	1.8582	0.3269	-0.2986	0.9821	-0.1888	1.4882	0.001	0.0343	0.0612	-0.0268	-0.0185	-0.1847	-0.1085	0.2707	0.0175	0.0837	-0.0101	0.0147	0.0745	-0.0052	0.0726	80.1348	66.6011	29.0851
6	0.7664	-0.1725	-0.6719	1.666	1.8233	2.4732	0.0739	0.1283	0.0643	-0.1568	-0.0633	0.0075	-0.1582	-0.1572	-0.0106	0.0718	0.0112	0.0011	0.0609	0.0204	0.0565	62.2251	77.9202	37.1073
7	12.0005	5.4137	3.4572	2.7771	-0.0054	8.3113	-0.1201	-0.2527	0.668	0.3419	-0.064	0.0705	-0.401	-0.197	0.1842	0.0986	-0.0027	0.0006	0.0566	0.0079	0.0778	72.7551	83.594	49.6051
8	0.3775	-0.0125	0.0396	1.1049	0.8033	0.957	-0.0115	0.0838	-0.002	-0.1251	-0.0605	0.1528	-0.096	-0.0988	0.072	0.0787	-0.0021	0.003	0.0897	0.0194	0.0685	62.0743	67.2644	27.0001
9	2.4944	0.705	-0.9284	2.5259	-0.8354	4.0775	0.0273	0.368	0.0738	-0.2293	0.0708	0.2086	-0.1859	-0.2136	-0.0981	0.0836	-0.0124	0.0102	0.1406	-0.0432	0.0755	65.9335	48.3964	12.3216
10	7.4637	-0.3053	-1.2236	1.0832	0.098	1.1376	-0.0234	0.225	-0.2705	-0.0628	-0.0014	0.0484	0.0818	-0.085	0.0248	0.0783	-0.0078	0.0181	0.0533	-0.0292	0.0705	76.4138	36.2008	19.383
11	2.0311	-0.2009	-0.766	2.123	0.0226	2.5558	-0.0619	-0.1641	-0.2213	0.1676	0.0307	-0.1189	0.2303	0.2076	0.0312	0.0587	-0.0005	0.0239	0.0677	-0.0176	0.115	79.1219	39.4438	28.3747
12	3.6659	0.1758	-1.3003	4.6697	3.1879	5.9845	-0.0853	0.0516	-0.2632	-0.0015	0.0593	-0.1705	0.1103	0.1834	0.0259	0.0718	-0.0025	-0.0025	0.0852	0.0226	0.0885	85.1653	45.7943	36.5933
13	1.4262	-0.995	0.2198	2.4167	-0.1478	0.6703	-0.0596	-0.0134	0.1581	0.0997	0.0243	0.0492	-0.1229	-0.0868	0.0352	0.0687	-0.0055	-0.0002	0.0883	-0.0036	0.0641	55.5221	80.0683	50.5676
14	5.3598	-0.8771	-0.5764	1.9441	0.4475	1.2706	-0.0421	0.0142	0.201	-0.0796	0.0215	0.0739	-0.0532	-0.0565	0.0206	0.0784	0.008	-0.0346	0.051	0.0459	0.0857	48.1557	92.4694	43.1076
15	2.0816	-0.9788	-0.1872	0.8386	0.0967	0.5034	-0.0117	0.1147	-0.0419	-0.0321	-0.0202	0.1158	-0.0306	-0.0747	0.0319	0.082	-0.0112	0.001	0.0697	0.0098	0.0686	58.1539	75.6334	43.267
16	3.623	-1.1147	-1.0943	2.5103	0.2532	0.3338	-0.1116	0.0728	-0.4584	-0.0512	0.0232	-0.014	0.4811	0.0829	0.0884	0.0962	-0.0132	-0.0012	0.0546	-0.0059	0.036	50.061	65.6626	49.6014
17	1.5586	-1.5204	-0.9145	2.0785	0.8796	0.6066	-0.0696	-0.0469	-0.1005	0.0389	0.0987	-0.0634	0.0646	0.0968	-0.0291	0.0696	-0.0021	0.0027	0.0779	0.0005	0.0564	73.3543	61.2544	46.3988
18	3.8737	1.071	0.9855	3.1169	0.1234	2.4048	0.0657	-0.0168	-0.2466	0.0443	-0.0173	-0.0405	0.2725	-0.0254	-0.0484	0.0818	0.0006	0.0343	0.0802	0.0064	0.0929	74.076	38.0781	39.9801
19	1.4365	-0.5779	-0.1734	1.1174	0.033	0.7327	-0.0358	0.089	-0.116	-0.0419	0.0119	-0.0585	0.0988	0.0519	0.0238	0.0716	-0.0028	0.0012	0.0812	0.0024	0.0483	70.2382	63.5427	52.3573
20	0.9115	-0.2555	-0.2761	0.9599	0.2887	1.5127	-0.0273	0.0585	-0.0272	-0.0312	0.0242	-0.1008	0.0219	0.0687	0.0031	0.0581	-0.0185	0.0235	0.0723	-0.0107	0.0912	83.4097	53.9269	25.0291

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	46 - 85	46 - 85
2	X-RAY DIFFRACTION	2	A	A	86 - 107	86 - 107
3	X-RAY DIFFRACTION	3	A	A	108 - 146	108 - 146
4	X-RAY DIFFRACTION	4	A	A	147 - 165	147 - 165
5	X-RAY DIFFRACTION	5	A	A	166 - 205	166 - 205
6	X-RAY DIFFRACTION	6	A	A	206 - 227	206 - 227
7	X-RAY DIFFRACTION	7	A	A	228 - 233	228 - 233
8	X-RAY DIFFRACTION	8	A	A	234 - 265	234 - 265
9	X-RAY DIFFRACTION	9	A	A	266 - 285	266 - 285
10	X-RAY DIFFRACTION	10	A	A	286 - 307	286 - 307
11	X-RAY DIFFRACTION	11	A	A	308 - 346	308 - 346
12	X-RAY DIFFRACTION	12	A	A	347 - 358	347 - 358
13	X-RAY DIFFRACTION	13	A	A	359 - 385	359 - 385
14	X-RAY DIFFRACTION	14	A	A	386 - 413	386 - 413
15	X-RAY DIFFRACTION	15	A	A	414 - 452	414 - 452
16	X-RAY DIFFRACTION	16	A	A	453 - 466	453 - 466
17	X-RAY DIFFRACTION	17	A	A	467 - 483	467 - 483
18	X-RAY DIFFRACTION	18	A	A	484 - 505	484 - 505
19	X-RAY DIFFRACTION	19	A	A	506 - 548	506 - 548
20	X-RAY DIFFRACTION	20	A	A	549 - 618	549 - 618

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