PDB-1tt0: Crystal Structure of Pyranose 2-Oxidase

ID or keywords:

Entry

Database: PDB / ID: 1tt0

Title

Crystal Structure of Pyranose 2-Oxidase

Components

pyranose oxidase

Keywords

OXIDOREDUCTASE / GMC OXIDOREDUCTASE / ALPHA/BETA STRUCTURE /

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 ochracea (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.8 Å

Authors

Hallberg, B.M. / Leitner, C. / Haltrich, D. / Divne, C.

Citation

Journal: J.Mol.Biol. / Year: 2004
Title: Crystal structure of the 270 kDa homotetrameric lignin-degrading enzyme pyranose 2-oxidase
Authors: Hallberg, B.M. / Leitner, C. / Haltrich, D. / Divne, C.

History

Deposition	Jun 21, 2004	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 21, 2005	Provider: repository / Type: Initial release
Revision 1.1	Apr 30, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Nov 12, 2014	Group: Structure summary
Revision 1.4	Feb 14, 2024	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_close_contact / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 600

HETEROGEN THE LIGANDS LABELED 12P DODECAETHYLENE GLYCOL ARE ACTUALLY MONOMETHYL ETHER PEG 2000 OF ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tt/1tt0 ftp://data.pdbj.org/pub/pdb/validation_reports/tt/1tt0	HTTPS FTP

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Related structure data

Similar structure data	4mok-d 3fdy-1 1tzl-2 2igm-2 4moe-d 2ign-2 1tzl-1 3k4n-1 3lsi-1 2igo-1 4mor-d 2igo-2 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

B: pyranose oxidase

C: pyranose oxidase

D: pyranose oxidase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	99.920, 101.690, 135.630
Angle α, β, γ (deg.)	90.00, 90.95, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Details

The biological assembly is a homotetramer. The complete homotetramer is contained within the asymmetric unit.

#1: Protein	pyranose oxidase / / pyranose-2-oxidase Mass: 69413.789 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Trametes ochracea (fungus) / Cellular location: hyphal periplasmic space / Strain: MB49 References: GenBank: 31044224, UniProt: Q7ZA32*PLUS, pyranose oxidase
#2: Chemical	ChemComp-ACT / ACETATE ION / Acetate Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Comment: FAD*YM
#4: Chemical	ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol Mass: 546.646 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C₂₄H₅₀O₁₃ / Comment: precipitant*YM
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 2495 / 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: 2.5 Å³/Da / Density % sol: 50 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.7 Details: mme PEG 2000, sodium acetate, magnesium chloride, Ta6Br12, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.2552 Å
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 4, 2002
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.2552 Å / Relative weight: 1
Reflection	Resolution: 1.8→38.3 Å / Num. all: 232099 / Num. obs: 232099 / % possible obs: 92.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / R_merge(I) obs: 0.113 / Net I/σ(I): 8
Reflection shell	Resolution: 1.8→1.9 Å / Redundancy: 2.1 % / R_merge(I) obs: 0.344 / Mean I/σ(I) obs: 2.8 / Num. unique all: 23512 / % possible all: 62.8

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Processing

Software

Name	Version	Classification
REFMAC	5.1.24	refinement
XDS		data scaling
SOLVE		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.8→30 Å / Cor.coef. F_o:F_c: 0.969 / Cor.coef. F_o:F_c free: 0.949 / SU B: 2.067 / SU ML: 0.062 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.17122	2331	1 %	RANDOM
R_work	0.13369	-	-	-
all	0.13407	229734	-	-
obs	0.13407	229734	92.58 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 12.918 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.33 Å²	0 Å²	0.1 Å²
2-	-	-0.1 Å²	0 Å²
3-	-	-	0.44 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18148	0	476	2495	21119

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.019	0.021	19154
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	16852
X-RAY DIFFRACTION	r_angle_refined_deg	1.775	1.953	25952
X-RAY DIFFRACTION	r_angle_other_deg	0.899	3	39231
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.811	5	2298
X-RAY DIFFRACTION	r_chiral_restr	0.157	0.2	2806
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	21012
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	3890
X-RAY DIFFRACTION	r_nbd_refined	0.212	0.2	3686
X-RAY DIFFRACTION	r_nbd_other	0.259	0.2	20205
X-RAY DIFFRACTION	r_nbtor_other	0.087	0.2	10442
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.163	0.2	1938
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.22	0.2	12
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.226	0.2	80
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.223	0.2	37
X-RAY DIFFRACTION	r_mcbond_it	1.094	1.5	11532
X-RAY DIFFRACTION	r_mcangle_it	1.922	2	18752
X-RAY DIFFRACTION	r_scbond_it	2.932	3	7622
X-RAY DIFFRACTION	r_scangle_it	4.783	4.5	7200

LS refinement shell

Resolution: 1.8→1.847 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.238	100
R_work	0.209	10293

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	0.707	-0.1247	-0.1554	1.2265	0.6523	0.9354	0.002	-0.0293	0.0409	0.0905	0.0248	-0.0134	0.0665	-0.0045	-0.0267	0.1093	0.0072	-0.0059	0.1088	-0.0115	0.1137	21.4132	55.5294	143.8255
2	0.4852	-0.1153	-0.0571	0.7997	0.2252	0.5773	0.0095	-0.0273	0.0225	0.0165	-0.0128	0.0995	-0.0576	-0.072	0.0033	0.0923	0.0008	-0.0016	0.1187	-0.0142	0.129	14.252	58.3742	137.4946
3	0.2817	-0.1828	-0.3046	0.4136	0.1987	0.8751	0.026	-0.0136	0.0988	0.018	0.0228	-0.0628	-0.0494	0.0194	-0.0488	0.1059	-0.0012	-0.0055	0.0963	-0.0219	0.1473	25.4894	66.9944	134.336
4	0.3777	-0.1147	-0.1028	0.2163	0.0623	0.4143	-0.0137	-0.0168	0.0347	0.0173	0.0272	-0.0582	-0.0082	0.0489	-0.0134	0.0888	-0.0109	-0.0136	0.1046	-0.0085	0.1441	41.692	53.099	126.722
5	0.5029	-0.0516	0.0921	0.3015	0.0736	0.1983	0.0307	0.0056	-0.0332	0.0063	0.0072	-0.0712	0.0052	0.0268	-0.0379	0.1021	-0.0026	-0.0062	0.1009	-0.0005	0.1374	39.4058	44.2697	114.5553
6	0.2894	0.4247	1.1682	0.404	0.1501	1.2291	0.0176	0.0583	-0.0188	0.0035	-0.0375	-0.0004	0.0568	0.0118	0.0199	0.1208	0.0001	-0.0035	0.1413	-0.0011	0.1492	29.0988	36.0983	130.1821
7	0.228	0.3072	0.1356	0.7811	0.2598	-0.152	-0.0279	-0.0035	0.0353	-0.091	0.0043	0.0158	-0.0322	-0.0144	0.0237	0.1257	0.0004	-0.0004	0.136	-0.0024	0.1134	7.8444	45.4485	110.5338
8	0.7089	-0.0928	0.2088	1.191	-0.2792	0.7014	0.0397	-0.0722	0.0343	0.0882	-0.022	-0.0586	-0.0498	-0.0042	-0.0176	0.1174	-0.0119	-0.0262	0.1149	0.0039	0.1024	25.5453	16.7156	146.7528
9	0.6228	-0.2456	-0.0029	0.8468	-0.2477	0.5285	0.0098	-0.0213	-0.0063	0.0051	-0.035	-0.1282	0.0426	0.038	0.0252	0.0964	-0.0088	-0.0252	0.113	0.0123	0.1265	31.9855	12.8193	140.3051
10	0.2499	-0.0127	0.1658	0.3548	-0.0835	0.649	0.0126	-0.0052	-0.0607	0.0279	-0.0204	-0.0262	0.0651	-0.017	0.0078	0.1126	-0.0115	-0.0137	0.1151	0.0172	0.1236	20.4482	4.069	139.5296
11	0.311	-0.1819	0.1715	0.24	0.046	0.5512	-0.0114	-0.0365	0.0088	0.0325	0	0.0272	0.0279	-0.1092	0.0114	0.099	-0.0173	0.0048	0.1276	0.0059	0.108	3.7072	17.0284	131.4905
12	0.3449	-0.2348	0.0169	0.3055	-0.0511	0.1243	0.0177	-0.0112	-0.01	-0.0166	-0.0106	0.0182	-0.0039	-0.0174	-0.0071	0.111	-0.0043	-0.0042	0.1197	-0.0003	0.1089	4.7523	23.7767	117.8132
13	0.338	-0.2412	-0.6675	0.519	-0.6696	0.7558	-0.0146	0.0359	0.058	0.0525	-0.0011	-0.0783	-0.0565	0.0478	0.0157	0.1249	-0.0081	-0.0163	0.1381	-0.0092	0.1447	16.6005	33.9622	130.9925
14	0.0977	0.1508	-0.1633	0.307	-0.1989	0.0515	-0.0034	-0.0095	-0.0184	-0.0237	0.004	-0.0554	0.031	0.0184	-0.0006	0.1169	-0.0029	0.0013	0.1203	-0.0001	0.1322	35.8365	21.605	111.1165
15	1.8348	0.65	-1.3412	2.3625	-0.2199	2.9707	0.0485	0.1852	0.0002	-0.153	0.0397	-0.1041	-0.0572	-0.0344	-0.0882	0.0943	0.0139	0.0467	0.1333	-0.0335	0.0504	38.3654	26.1001	59.8371
16	1.1679	-0.3774	-0.0657	1.1174	-0.1391	0.9572	-0.0447	0.0821	-0.1774	-0.1579	0.0271	-0.1273	0.1347	0.0783	0.0175	0.1661	-0.0123	0.0902	0.1054	-0.0504	0.1191	41.2877	18.7074	66.2204
17	0.6495	-0.1206	-0.1132	0.5072	0.5256	0.9897	-0.0171	0.0942	-0.0021	-0.1498	0.0196	-0.2251	-0.0199	0.0914	-0.0026	0.1421	-0.0069	0.1147	0.1096	-0.0219	0.1428	51.1824	29.2456	66.7833
18	0.4792	-0.133	-0.0028	0.6574	0.2794	0.564	0.0354	0.0991	0.0636	-0.1886	0.0015	-0.1235	-0.1033	0.0314	-0.0369	0.1408	-0.0196	0.0676	0.097	0.0216	0.1093	40.0283	47.6791	73.7888
19	0.3578	-0.2007	-0.0714	0.5749	0.0381	0.2899	-0.0043	0.0569	0.046	-0.0786	0.0146	-0.0572	-0.0503	-0.0106	-0.0103	0.1197	-0.0082	0.0259	0.1103	0.0093	0.1048	32.7724	47.849	87.2598
20	1.5121	-0.4423	-0.0362	1.1935	-0.7936	2.763	-0.0126	0.0184	-0.042	0.0521	-0.0376	-0.0103	-0.1555	-0.0119	0.0502	0.1104	-0.0247	0.0176	0.0987	-0.0151	0.0879	21.6328	36.6753	74.233
21	0.4078	0.2248	-0.4168	0.3293	-0.2678	0.0446	-0.0038	-0.0135	-0.0284	-0.0312	0.0075	-0.0539	0.0099	-0.0253	-0.0036	0.1217	-0.0036	0.0127	0.1258	-0.0155	0.1147	31.3909	17.0958	95.2031
22	0.8259	-0.0018	0.5386	0.3317	0.2157	1.0536	0.0296	0.02	-0.0239	-0.1013	-0.0025	0.0038	-0.0827	-0.0308	-0.0271	0.1658	0.0164	-0.0152	0.1337	-0.0033	0.0605	-0.1285	32.7445	61.3459
23	0.9094	-0.1052	0.1291	0.6709	0.0059	0.8324	-0.013	0.0386	0.1031	-0.0853	0.0002	0.0176	-0.1414	-0.0792	0.0128	0.1628	0.0097	-0.0331	0.1106	0.0113	0.0607	-2.4721	41.1079	66.7041
24	0.438	-0.0134	0.24	0.2738	-0.1871	0.7934	-0.0019	0.0237	-0.0254	-0.0607	-0.015	0.0927	-0.0074	-0.08	0.0169	0.1341	0.0179	-0.0387	0.1345	-0.0036	0.0917	-12.0943	30.8852	70.0339
25	0.154	-0.2541	-0.0321	0.2874	-0.1378	0.778	0.048	0.032	-0.0698	-0.0573	-0.0205	0.0414	0.072	-0.0348	-0.0274	0.1291	-0.0106	-0.0269	0.1038	-0.0183	0.1012	-0.1149	13.715	78.7577
26	0.2724	-0.1142	0.194	0.6283	0.0413	0.3151	0.028	0.0319	-0.05	-0.0458	0.0207	-0.0403	0.0433	0.0073	-0.0487	0.1199	-0.0017	-0.0019	0.1236	-0.0115	0.1008	8.5744	15.6852	91.1872
27	1.2743	-0.3951	0.7973	1.8532	0.9636	2.6253	0.0252	0.0983	-0.038	0.0085	-0.0505	-0.0094	-0.0038	0.0985	0.0253	0.115	-0.022	0.0168	0.1409	0.0035	0.1116	18.1873	24.4933	75.4002
28	0.6871	0.3325	0.3691	0.2438	0.0731	0.0077	-0.0149	-0.0361	0.0392	-0.0394	0.0024	-0.001	-0.0007	0.0155	0.0126	0.135	0.0033	0.0026	0.1313	0.0034	0.0994	10.565	47.3398	93.7712
29	4.988	-3.7979	-6.9538	2.2099	3.157	5.6694	-0.1094	0.1532	-0.1363	0.0276	0.0324	-0.0174	0.0779	-0.1043	0.077	0.1039	-0.0009	-0.0226	0.1022	0.001	0.1127	24.2045	51.0254	129.1454
30	5.3201	-0.4443	5.2492	1.2372	-1.2912	3.5331	0.0745	0.2012	0.0613	-0.0652	-0.0361	-0.0357	0.0675	0.1663	-0.0384	0.1081	-0.0017	-0.0116	0.1047	-0.0022	0.1005	21.3326	19.0453	131.931
31	0.4742	-2.302	-2.286	8.0268	8.4564	6.6171	0.0362	-0.0044	0.045	-0.0445	-0.1463	0.2346	0.0455	-0.1445	0.1101	0.1034	0.0014	0.0003	0.1026	-0.0017	0.1027	36.0104	30.3592	74.0228
32	-0.0101	-1.3196	1.2318	7.1891	-4.9908	5.6935	-0.0022	-0.0649	0.0885	-0.0257	0.0924	-0.0939	-0.0265	-0.0507	-0.0903	0.1028	0.0122	-0.008	0.1056	0.0009	0.1025	3.7774	30.8411	75.6953
33	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.1033	0	0	0.1033	0	0.1033	33.4451	49.2181	121.1713
34	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.1033	0	0	0.1033	0	0.1033	11.2473	19.8177	124.6749
35	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.1033	0	0	0.1033	0	0.1033	36.2884	40.6888	80.8901
36	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.1033	0	0	0.1033	0	0.1033	4.3945	21.7238	84.0894

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	44 - 79	44 - 79
2	X-RAY DIFFRACTION	2	A	A	254 - 353	254 - 353
3	X-RAY DIFFRACTION	3	A	A	552 - 618	552 - 618
4	X-RAY DIFFRACTION	4	A	A	159 - 253	159 - 253
5	X-RAY DIFFRACTION	5	A	A	354 - 551	354 - 551
6	X-RAY DIFFRACTION	6	A	A	80 - 110	80 - 110
7	X-RAY DIFFRACTION	7	A	A	111 - 158	111 - 158
8	X-RAY DIFFRACTION	8	B	B	44 - 79	44 - 79
9	X-RAY DIFFRACTION	9	B	B	254 - 353	254 - 353
10	X-RAY DIFFRACTION	10	B	B	552 - 618	552 - 618
11	X-RAY DIFFRACTION	11	B	B	159 - 253	159 - 253
12	X-RAY DIFFRACTION	12	B	B	354 - 551	354 - 551
13	X-RAY DIFFRACTION	13	B	B	80 - 110	80 - 110
14	X-RAY DIFFRACTION	14	B	B	111 - 158	111 - 158
15	X-RAY DIFFRACTION	15	C	C	46 - 79	46 - 79
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