PDB-3lsi: Pyranose 2-oxidase T169A, tetragonal

ID or keywords:

Entry

Database: PDB / ID: 3lsi

Title

Pyranose 2-oxidase T169A, tetragonal

Components

Pyranose 2-oxidase

Keywords

OXIDOREDUCTASE / GMC oxidoreductase / T169A mutant / Rossmann fold / PHBH fold / homotetramer / non-covalent FAD

Function / homology

Function and homology information

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

Biological species

Trametes ochracea (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 1.9 Å

Authors

Tan, T.C. / Spadiut, O. / Divne, C.

Citation

Journal: J.Mol.Biol. / Year: 2010
Title: H-bonding and positive charge at the N5/O4 locus are critical for covalent flavin attachment in trametes pyranose 2-oxidase.
Authors: Tan, T.C. / Pitsawong, W. / Wongnate, T. / Spadiut, O. / Haltrich, D. / Chaiyen, P. / Divne, C.

History

Deposition	Feb 12, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 25, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 1, 2017	Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site / _software.name
Revision 1.3	Oct 13, 2021	Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Feb 21, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3lsi.cif.gz	469.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3lsi.ent.gz	383.5 KB	Display	PDB format
PDBx/mmJSON format	3lsi.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3lsi_validation.pdf.gz	916.1 KB	Display	wwPDB validaton report
Full document	3lsi_full_validation.pdf.gz	935.6 KB	Display
Data in XML	3lsi_validation.xml.gz	52.9 KB	Display
Data in CIF	3lsi_validation.cif.gz	79 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ls/3lsi ftp://data.pdbj.org/pub/pdb/validation_reports/ls/3lsi	HTTPS FTP

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Related structure data

Related structure data	3lshC 3lskC 3lsmC C: citing same article (ref.)
Similar structure data	4moi-1 3k4m-1 2igo-1 3lsh-d 4mom-d 2ign-1 1tt0-d 4moe-d 3fdy-1 1tzl-1 2ign-2 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 2-oxidase

B: Pyranose 2-oxidase

hetero molecules

140 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Pyranose 2-oxidase

B: Pyranose 2-oxidase

hetero molecules

A: Pyranose 2-oxidase

B: Pyranose 2-oxidase

hetero molecules

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

Unit cell

Length a, b, c (Å)	101.298, 101.298, 249.768
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

#1: Protein	Pyranose 2-oxidase / Pyranose oxidase Mass: 69383.758 Da / Num. of mol.: 2 / Mutation: T169A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trametes ochracea (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 Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Comment: FAD*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1004 / 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: 2.31 Å³/Da / Density % sol: 46.72 %
Crystal grow	Temperature: 298 K / pH: 5.2 Details: 0.1M MES, 0.050M MgCl2, 10% (W/V)% monomethylether PEG 2000, 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: I911-2 / Wavelength: 1.03908
Detector	Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 19, 2009 / Details: MIRRORS
Radiation	Monochromator: BENT SI (111) CRYSTAL, HORIZONTALLY FOCUSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.03908 Å / Relative weight: 1
Reflection	Resolution: 1.9→29.1 Å / Num. obs: 102585 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / R_sym value: 0.115 / Net I/σ(I): 10.9
Reflection shell	Resolution: 1.9→2 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 2.8 / R_sym value: 0.578 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
MAR345		data collection
FFT		model building
CCP4		model building
REFMAC	5.5.0066	refinement
XDS		data reduction
XSCALE		data scaling
FFT		phasing
CCP4		phasing

Refinement

Method to determine structure:

FOURIER SYNTHESIS / Resolution: 1.9→29.1 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.929 / SU B: 6.521 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.213	3090	3 %	RANDOM
R_work	0.164	-	-	-
obs	0.166	99494	99.6 %	-

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: 11.64 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.43 Å²	0 Å²	0 Å²
2-	-	-0.43 Å²	0 Å²
3-	-	-	0.87 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→29.1 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9072	0	106	1004	10182

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.021	0.022	9420
X-RAY DIFFRACTION	r_bond_other_d	0	0.02	8177
X-RAY DIFFRACTION	r_angle_refined_deg	1.904	1.96	12814
X-RAY DIFFRACTION	r_angle_other_deg	0.824	3	19117
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.019	5	1149
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.387	24.489	450
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.809	15	1513
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.444	15	54
X-RAY DIFFRACTION	r_chiral_restr	0.152	0.2	1393
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.021	10471
X-RAY DIFFRACTION	r_gen_planes_other	0	0.02	1885
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.058	1.5	5751
X-RAY DIFFRACTION	r_mcbond_other	0.345	1.5	2308
X-RAY DIFFRACTION	r_mcangle_it	1.723	2	9344
X-RAY DIFFRACTION	r_scbond_it	2.771	3	3669
X-RAY DIFFRACTION	r_scangle_it	4.196	4.5	3470
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.9→2 Å / Total num. of bins used: 10

	R_factor	Num. reflection	% reflection
R_free	0.252	438	-
R_work	0.2	14306	-
obs	-	-	99.77 %

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	0.8982	-0.2632	0.1727	0.9479	0.0439	0.6199	0.0517	0.0903	-0.0022	-0.145	-0.0381	-0.0666	0.0818	0.0702	-0.0136	0.075	0.0134	0.0157	0.0711	-0.0008	0.0524	2.133	15.4	-42.688
2	0.1107	-0.1406	0.0941	0.1934	-0.117	0.0814	0.0134	0.0092	-0.0111	0.0151	-0.0108	0.0115	0.0188	0.008	-0.0026	0.0759	0.0007	0.0084	0.0767	0.0067	0.0581	6.24	7.032	-15.82
3	0.7152	-0.0624	-0.0137	1.5343	-0.4463	1.2225	-0.0035	0.0347	0.0689	0.0081	0.0317	0.0505	-0.1262	-0.0757	-0.0282	0.062	0.0101	-0.0037	0.0989	0.0073	0.0698	-14.726	26.839	-31.692
4	1.4568	0.1656	-0.0491	0.9265	-0.1409	0.7313	-0.0457	-0.0009	0.0267	0.0138	0.0362	0.0351	-0.027	-0.0979	0.0095	0.0783	0.0025	-0.0274	0.0878	0.0083	0.0692	-25.657	10.541	-22.302
5	0.5965	0.2864	-0.0216	0.8921	-0.1635	0.4807	-0.0228	0.1097	-0.0798	-0.1285	0.0091	-0.1007	0.0624	0.0695	0.0138	0.0601	0.0215	0.0144	0.0675	-0.0009	0.0215	6.497	15.779	-42.411
6	0.7959	-0.0322	-0.203	0.9804	-0.0592	0.9675	0.0114	-0.0351	0.0674	0.0271	-0.02	-0.1757	-0.1162	0.1895	0.0086	0.0361	-0.0069	-0.0067	0.0729	0.0161	0.0696	10.743	27.499	-28.584
7	0.7176	0.5826	0.1416	0.6668	0.074	0.2732	0.0324	-0.0005	-0.007	0.0227	-0.023	0.0485	0.0337	-0.0413	-0.0094	0.05	0.0013	-0.001	0.0629	-0.0028	0.0418	-29.798	1.773	-15.485
8	8.1854	13.4369	-1.7839	22.116	-2.9276	0.4068	-0.2578	0.0012	-0.2382	-0.5282	0.1036	-0.377	0.0654	0.0122	0.1543	0.2528	-0.0285	0.0213	0.2903	0.0677	0.5043	-10.469	-0.002	-10.663
9	0.4304	0.0463	-0.1471	0.3774	-0.1061	0.2487	0.0333	0.0022	0.0459	0.0268	-0.0245	-0.0211	-0.0314	0.0323	-0.0089	0.0745	-0.0006	-0.0152	0.0739	-0.0012	0.0361	-5.044	19.051	-12.404
10	0.3133	0.0696	-0.0989	0.4611	-0.3605	0.9731	-0.0225	0.0311	0.0267	-0.0383	-0.006	-0.0428	-0.0046	-0.0099	0.0285	0.064	0.0111	-0.0015	0.0624	0.0116	0.0587	-2.056	28.265	-31.677
11	1.3172	0.0738	-0.617	1.3808	0.539	1.5147	0.0247	0.2175	-0.0242	-0.2559	-0.0428	0.1203	-0.1135	-0.1097	0.0181	0.086	0.0136	-0.0326	0.0818	-0.0277	0.0232	-2.031	-19.358	-42.291
12	0.1621	-0.0874	-0.1089	0.1516	0.111	0.1052	0.019	0.0119	-0.0092	0.0077	-0.0224	0.0028	-0.0215	-0.0106	0.0035	0.0683	0.0014	-0.0094	0.0577	-0.012	0.0463	-6.15	-8.588	-16.536
13	0.5448	-0.1901	0.0459	2.5642	-0.2551	1.577	-0.0284	0.0525	-0.1204	-0.1338	0.0117	-0.0089	0.2824	0.0878	0.0167	0.0718	0.0137	0.0091	0.0827	-0.0249	0.0698	14.854	-30.016	-29.503
14	1.2077	0.3169	0.1774	1.0555	0.1698	2.5769	-0.0258	-0.0022	-0.053	-0.0143	-0.0101	-0.065	0.0093	0.1325	0.0358	0.037	0.0069	0.0249	0.0672	-0.009	0.061	26.049	-14.24	-19.893
15	0.7475	0.2725	0.3204	0.8257	0.2574	0.4194	-0.0281	0.1658	0.0318	-0.1469	-0.0022	0.0451	-0.0304	0.0222	0.0303	0.0805	0.0031	-0.014	0.0829	-0.0182	0.0242	0.568	-16.24	-41.179
16	1.1848	0.0569	0.099	1.1396	0.408	1.7246	-0.0111	0.053	-0.1058	-0.033	-0.0763	0.2148	0.151	-0.2525	0.0874	0.0408	-0.0171	-0.0263	0.0736	-0.0603	0.1104	-13.408	-26.76	-32.341
17	0.8001	0.5079	0.1549	0.6182	0.0948	0.3244	-0.0046	-0.008	-0.0394	-0.0019	-0.0177	-0.035	-0.0289	0.0425	0.0223	0.093	0.0045	0.0135	0.0832	-0.003	0.0579	19.747	-12.098	-11.421
18	1.1086	0.8971	-0.0832	1.2518	-0.0012	0.3227	0.0034	0.0013	0.0426	-0.0072	-0.0344	-0.0181	-0.0514	0.0605	0.031	0.069	0.0028	0.0034	0.0798	0.0128	0.0253	29.642	-3.327	-15.962
19	3.3523	8.289	2.9653	20.5003	7.3337	2.628	-0.3668	0.0824	0.2121	-0.8772	0.2065	0.5344	-0.3081	0.063	0.1603	0.2233	0.0338	-0.0414	0.1394	-0.0178	0.3407	10.05	-1.577	-10.264
20	0.4257	0.1097	0.0534	0.3194	0.1253	0.3649	-0.0056	0.0474	-0.0837	-0.0248	-0.0235	0.0422	0.0422	-0.0139	0.0291	0.0546	0.003	0.0004	0.0388	-0.0178	0.054	3.401	-25.724	-20.846

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	44 - 85
2	X-RAY DIFFRACTION	2	A	86 - 166
3	X-RAY DIFFRACTION	3	A	167 - 208
4	X-RAY DIFFRACTION	4	A	209 - 252
5	X-RAY DIFFRACTION	5	A	253 - 307
6	X-RAY DIFFRACTION	6	A	308 - 359
7	X-RAY DIFFRACTION	7	A	360 - 455
8	X-RAY DIFFRACTION	8	A	456 - 462
9	X-RAY DIFFRACTION	9	A	463 - 537
10	X-RAY DIFFRACTION	10	A	538 - 618
11	X-RAY DIFFRACTION	11	B	43 - 82
12	X-RAY DIFFRACTION	12	B	83 - 166
13	X-RAY DIFFRACTION	13	B	167 - 206
14	X-RAY DIFFRACTION	14	B	207 - 246
15	X-RAY DIFFRACTION	15	B	247 - 293
16	X-RAY DIFFRACTION	16	B	294 - 349
17	X-RAY DIFFRACTION	17	B	350 - 384
18	X-RAY DIFFRACTION	18	B	385 - 455
19	X-RAY DIFFRACTION	19	B	456 - 462
20	X-RAY DIFFRACTION	20	B	463 - 618

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