PDB-4mif: Pyranose 2-oxidase from Phanerochaete chrysosporium, wild type fr...

ID or keywords:

Entry

Database: PDB / ID: 4mif

Title

Pyranose 2-oxidase from Phanerochaete chrysosporium, wild type from natural source

Components

Pyranose 2-oxidase

Keywords

OXIDOREDUCTASE / GMC OXIDOREDUCTASE / ROSSMANN FOLD / PHBH FOLD / PYRANOSE 2-OXIDASE / SUGAR OXIDOREDUCTASE / FLAVINYLATION / HYPHAE

Function / homology

Function and homology information

pyranose oxidase / pyranose oxidase activity / flavin adenine dinucleotide binding / periplasmic space
Similarity search - Function

Biological species

Phanerochaete chrysosporium (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Hassan, N. / Tan, T.C. / Spadiut, O. / Pisanelli, I. / Fusco, L. / Haltrich, D. / Peterbauer, C. / Divne, C.

Citation

Journal: FEBS Open Bio / Year: 2013
Title: Crystal structures of Phanerochaete chrysosporium pyranose 2-oxidase suggest that the N-terminus acts as a propeptide that assists in homotetramer assembly.
Authors: Hassan, N. / Tan, T.C. / Spadiut, O. / Pisanelli, I. / Fusco, L. / Haltrich, D. / Peterbauer, C.K. / Divne, C.

History

Deposition	Aug 31, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 11, 2013	Provider: repository / Type: Initial release
Revision 1.1	Nov 15, 2017	Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site / _software.name
Revision 1.2	Sep 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id / _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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Download

PDBx/mmCIF format	4mif.cif.gz	925.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4mif.ent.gz	769.3 KB	Display	PDB format
PDBx/mmJSON format	4mif.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4mif_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	4mif_full_validation.pdf.gz	1.5 MB	Display
Data in XML	4mif_validation.xml.gz	97.3 KB	Display
Data in CIF	4mif_validation.cif.gz	141 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mi/4mif ftp://data.pdbj.org/pub/pdb/validation_reports/mi/4mif	HTTPS FTP

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Related structure data

Related structure data	4migC 4mihC 3pl8S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4mih-1 4mih-2 4mig-d 3bly-1 5opk-1 6je4-4 3tg7-1 3lsm-1 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 2-oxidase

B: Pyranose 2-oxidase

C: Pyranose 2-oxidase

D: Pyranose 2-oxidase

hetero molecules

280 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)	164.034, 164.034, 232.521
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

#1: Protein	Pyranose 2-oxidase / P2O / P2Ox / POD / POx / PROD / Pyranose oxidase / FAD-oxidoreductase / Glucose 2-oxidase / ...P2O / P2Ox / POD / POx / PROD / Pyranose oxidase / FAD-oxidoreductase / Glucose 2-oxidase / Pyranose:oxygen 2-oxidoreductase Mass: 69324.398 Da / Num. of mol.: 4 / Fragment: PYRANOSE 2-OXIDASE / Source method: isolated from a natural source / Source: (natural) Phanerochaete chrysosporium (fungus) / Strain: K-3 / References: UniProt: Q6QWR1, pyranose oxidase
#2: Chemical	ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE Mass: 787.566 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₇H₃₅N₉O₁₅P₂
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1562 / 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: 3.25 Å³/Da / Density % sol: 62.18 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: 0.1 M MES, 0.2 M MgCl2, 32% (w/v) PEG 400, 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: MAX II / Beamline: I911-3 / Wavelength: 1 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 22, 2008 / Details: mirrors
Radiation	Monochromator: double-crystal monochromator, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.8→47.43 Å / Num. all: 331914 / Num. obs: 331914 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.1 % / Net I/σ(I): 17.1
Reflection shell	Resolution: 1.8→1.9 Å / Redundancy: 11.2 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 49157 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
MAR345		data collection
PHASER		phasing
REFMAC	5.6.0117	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb entry 3PL8

3pl8

Resolution: 1.8→46.4 Å / Cor.coef. F_o:F_c: 0.972 / Cor.coef. F_o:F_c free: 0.965 / SU B: 3.238 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.078 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.171	1999	-	RANDOM
R_work	0.15261	-	-	-
obs	0.15273	329915	99.9 %	-
all	-	329915	-	-

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: 29.711 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.07 Å²	-0.04 Å²	0 Å²
2-	-	-0.07 Å²	0 Å²
3-	-	-	0.11 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→46.4 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18148	0	213	1562	19923

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.025	0.02	18947
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	12830
X-RAY DIFFRACTION	r_angle_refined_deg	2.226	1.961	25805
X-RAY DIFFRACTION	r_angle_other_deg	1.115	3	31181
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.719	5	2298
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.242	23.739	888
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.471	15	2985
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.56	15	126
X-RAY DIFFRACTION	r_chiral_restr	0.212	0.2	2812
X-RAY DIFFRACTION	r_gen_planes_refined	0.013	0.021	20918
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3885

LS refinement shell

Resolution: 1.8→1.897 Å / Total num. of bins used: 10

	R_factor	Num. reflection	% reflection
R_free	0.248	281	-
R_work	0.228	46084	-
obs	-	-	99.7 %

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	1.7719	-0.1092	0.832	0.8803	-0.2565	1.9849	0.0714	-0.0653	-0.2133	-0.0305	-0.0002	0.1127	0.2263	-0.1576	-0.0712	0.0745	0.0048	-0.0131	0.1232	-0.0208	0.1185	-7.295	-81.1298	11.7979
2	0.4425	0.0566	-0.0245	0.2498	-0.0337	0.2223	0.0186	0.1063	0.0672	-0.0314	-0.0035	0.0629	-0.0542	-0.0769	-0.0151	0.0469	0.0206	-0.0189	0.1119	0.0128	0.0782	-2.4717	-61.5121	15.3727
3	2.233	-0.0885	0.024	5.1324	-0.5242	2.0477	-0.0042	-0.1394	0.1744	0.4121	-0.0016	0.1808	-0.1125	-0.0463	0.0057	0.0413	0.0157	0.0185	0.178	0.003	0.0792	-10.8633	-66.2161	32.3563
4	0.5913	0.1007	0.1069	0.7569	0.0221	1.0449	0.0093	0.2235	-0.0559	-0.2327	0.0077	0.0826	0.0553	-0.0436	-0.017	0.0887	0.029	-0.0458	0.1864	-0.0056	0.0743	-6.374	-70.3065	-2.4702
5	1.2028	-0.2293	0.136	1.1088	-0.6029	1.2121	0.0577	-0.0303	-0.0828	-0.046	-0.1163	-0.0598	0.1058	0.181	0.0586	0.0397	-0.0006	0.0038	0.1067	-0.001	0.0735	-1.7034	-66.5804	39.4033
6	0.5363	0.0843	0.1229	0.4082	0.0701	0.5863	0.0204	0.1406	0.0221	-0.1095	-0.0074	0.0708	-0.0443	-0.0397	-0.013	0.0414	0.0322	-0.0231	0.1144	0.0258	0.057	-4.8874	-57.5163	9.129
7	0.2618	-0.035	-0.0254	0.9284	0.2385	0.3915	0.0091	0.0921	-0.0708	-0.1584	-0.0306	0.1096	0.0297	-0.0638	0.0215	0.0607	-0.0112	-0.0209	0.1175	-0.0174	0.115	5.942	-89.5846	18.406
8	0.4964	0.0286	0.0047	0.3414	0.0884	0.5714	0.0128	0.0403	-0.1137	-0.0203	0	-0.0349	0.0511	0.0446	-0.0128	0.055	-0.0041	-0.0139	0.0539	-0.0247	0.0976	25.0037	-96.1631	17.9409
9	2.1338	0.4892	-0.0223	1.172	-0.1	1.1938	0.0456	0.2271	-0.0073	-0.0906	0.0122	-0.0005	0.0128	0.0053	-0.0578	0.1596	0.0116	-0.0194	0.1442	-0.0549	0.1275	16.8673	-95.6806	6.0464
10	1.4279	0.3492	-0.0856	0.8329	-0.1259	0.7828	0.0335	-0.1873	-0.1648	0.1504	-0.0309	0.1265	0.0547	-0.1587	-0.0026	0.0658	-0.0198	0.0084	0.0652	0.0123	0.1099	7.983	-102.1602	35.2413
11	0.6817	-0.0906	0.1196	1.7817	-0.7583	1.6196	-0.0089	0.1335	0.0233	-0.1414	0.0506	0.0925	-0.1277	-0.102	-0.0417	0.0923	-0.0096	-0.0054	0.1433	-0.0188	0.0784	29.797	-79.6345	1.8914
12	0.6216	0.2288	-0.0859	0.5663	-0.1247	0.4817	0.0157	-0.0556	-0.1329	0.0503	-0.0193	0.0197	0.0605	-0.0132	0.0036	0.0536	-0.0029	-0.0149	0.0467	-0.0059	0.0944	23.9556	-97.0712	27.5273
13	0.2689	-0.0156	-0.0621	0.7116	0.3339	0.7443	0.0433	-0.0022	0.1018	-0.0494	0.0119	-0.0728	-0.2058	0.0939	-0.0552	0.0741	-0.042	0.0159	0.1342	-0.0049	0.0905	40.5783	-43.6842	43.563
14	0.4175	0.084	0.0379	0.474	-0.066	0.5324	0.0368	-0.0501	0.0903	0.0367	-0.0132	0.0558	-0.1288	-0.0485	-0.0236	0.0746	-0.0133	0.0267	0.082	-0.0199	0.0641	22.5973	-37.9661	47.7705
15	1.7876	0.2925	0.2918	1.0953	-0.1339	1.3248	0.0829	0.0917	0.2072	-0.0365	-0.0543	0.0638	-0.173	0.0355	-0.0286	0.1691	-0.0216	0.0555	0.0636	-0.0112	0.1107	30.8282	-28.4275	40.8729
16	0.87	0.0725	0.2598	0.5739	-0.0767	1.4793	0.0722	-0.1372	-0.0674	0.0831	-0.035	-0.1136	0.0439	0.2194	-0.0373	0.0517	-0.0408	-0.0033	0.113	-0.0127	0.0374	39.2278	-48.3546	63.1206
17	0.5994	0.1209	-0.2884	1.029	-0.153	2.4477	0.0009	0.0762	0.1152	-0.1824	0.0015	-0.0343	-0.1408	0.1187	-0.0023	0.1143	0.0026	0.0111	0.0849	0.033	0.1131	18.0057	-34.3645	25.0407
18	0.44	0.0866	0.1462	0.3309	-0.0012	0.6713	0.0432	-0.0972	0.0139	0.0572	-0.0141	-0.0024	-0.0528	0.015	-0.0292	0.0596	-0.0212	0.0201	0.0828	-0.0158	0.0401	23.4732	-45.0691	54.2897
19	1.0355	0.1571	-0.097	0.6416	-0.2943	0.8029	0.0643	-0.2273	0.0457	0.1564	-0.0423	-0.0571	-0.0969	0.0491	-0.022	0.0571	-0.0161	0.0168	0.073	-0.0066	0.0728	54.0031	-42.5639	31.8335
20	3.9594	0.7383	-2.24	1.4187	-0.4517	1.9587	0.0395	0.2073	0.1454	-0.1176	0.005	-0.1377	-0.1711	0.0219	-0.0445	0.0582	-0.0054	0.0035	0.094	0.0279	0.0491	17.4009	-45.3944	12.6495
21	0.3238	-0.0184	0.012	0.448	-0.1916	0.4408	0.0338	-0.0158	-0.0028	-0.0029	-0.0185	-0.0644	-0.0074	0.0477	-0.0153	0.0341	-0.0158	0.016	0.0871	0.0048	0.0811	58.462	-52.4024	22.3831
22	0.5137	0.2832	-0.1707	1.1949	-0.4619	0.7752	0.0408	-0.0074	0.0422	0.0061	-0.0028	-0.0366	-0.0504	0.0059	-0.0381	0.0712	-0.0049	0.0146	0.1515	-0.0143	0.1258	51.5531	-53.8968	21.2537
23	1.6752	0.2415	-1.5751	0.812	-0.519	3.4159	0.1422	-0.0633	0.0572	0.1689	0.0052	0.1002	-0.1701	-0.2487	-0.1474	0.0664	-0.0179	-0.0015	0.0951	0.0173	0.0856	47.256	-70.0441	33.9804
24	0.3875	0.1663	-0.0931	0.6407	-0.1492	0.2913	0.0285	0.0528	0.0486	-0.0765	-0.0095	-0.0395	-0.0339	-0.0049	-0.019	0.0463	-0.0051	0.0233	0.075	0.0164	0.0634	52.9051	-53.3815	11.9075

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	13 - 100
2	X-RAY DIFFRACTION	2	A	101 - 228
3	X-RAY DIFFRACTION	3	A	229 - 254
4	X-RAY DIFFRACTION	4	A	255 - 392
5	X-RAY DIFFRACTION	5	A	393 - 478
6	X-RAY DIFFRACTION	6	A	479 - 617
7	X-RAY DIFFRACTION	7	B	13 - 124
8	X-RAY DIFFRACTION	8	B	125 - 228
9	X-RAY DIFFRACTION	9	B	229 - 274
10	X-RAY DIFFRACTION	10	B	275 - 390
11	X-RAY DIFFRACTION	11	B	391 - 478
12	X-RAY DIFFRACTION	12	B	479 - 617
13	X-RAY DIFFRACTION	13	C	13 - 124
14	X-RAY DIFFRACTION	14	C	125 - 228
15	X-RAY DIFFRACTION	15	C	229 - 274
16	X-RAY DIFFRACTION	16	C	275 - 390
17	X-RAY DIFFRACTION	17	C	391 - 478
18	X-RAY DIFFRACTION	18	C	479 - 617
19	X-RAY DIFFRACTION	19	D	13 - 106
20	X-RAY DIFFRACTION	20	D	107 - 131
21	X-RAY DIFFRACTION	21	D	132 - 309
22	X-RAY DIFFRACTION	22	D	310 - 419
23	X-RAY DIFFRACTION	23	D	420 - 478
24	X-RAY DIFFRACTION	24	D	479 - 617

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