PDB-3lsh: Pyranose 2-oxidase T169A, monoclinic

ID or keywords:

Entry

Database: PDB / ID: 3lsh

Title

Pyranose 2-oxidase T169A, monoclinic

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 / 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 /

FOURIER SYNTHESIS / Resolution: 1.9 Å

Authors

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

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	3lsh.cif.gz	927.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3lsh.ent.gz	771.4 KB	Display	PDB format
PDBx/mmJSON format	3lsh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

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

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Related structure data

Related structure data	3lsiC 3lskC 3lsmC C: citing same article (ref.)
Similar structure data	2igo-1 3bg6-1 2ign-1 4mom-d 3lsi-1 2ign-2 3k4m-1 1tzl-1 4mok-d 4moe-d 4moj-d 3k4n-1 2igo-2 3k4k-1 3fdy-1 3k4j-1 1tzl-2 4moi-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

281 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)	100.403, 102.731, 137.817
Angle α, β, γ (deg.)	90.00, 91.02, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Pyranose 2-oxidase / Pyranose oxidase Mass: 69383.758 Da / Num. of mol.: 4 / Fragment: Pyranose 2-oxidase / 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 / Flavin adenine dinucleotide Mass: 785.550 Da / Num. of mol.: 4 / 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.: 1818 / 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: 2.56 Å³/Da / Density % sol: 51.96 %
Crystal grow	Temperature: 298 K / pH: 5.2 Details: 0.1M MES, 50MM 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→28.5 Å / Num. obs: 217370 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / R_sym value: 0.094 / Net I/σ(I): 12.7
Reflection shell	Resolution: 1.9→2 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.7 / R_sym value: 0.566 / % possible all: 98.4

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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→28.5 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.927 / SU B: 8.351 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.246	3217	1.5 %	RANDOM
R_work	0.195	-	-	-
obs	0.195	214152	98.8 %	-

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: 14.3 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.05 Å²	0 Å²	-0.29 Å²
2-	-	-0.47 Å²	0 Å²
3-	-	-	1.52 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→28.5 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18135	0	224	1818	20177

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.022	0.022	18844
X-RAY DIFFRACTION	r_bond_other_d	0	0.02	16364
X-RAY DIFFRACTION	r_angle_refined_deg	1.968	1.961	25634
X-RAY DIFFRACTION	r_angle_other_deg	0.815	3	38258
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.206	5	2297
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.348	24.477	898
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.689	15	3025
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.101	15	108
X-RAY DIFFRACTION	r_chiral_restr	0.156	0.2	2787
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.021	20935
X-RAY DIFFRACTION	r_gen_planes_other	0	0.02	3769
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	1.099	1.5	11498
X-RAY DIFFRACTION	r_mcbond_other	0.347	1.5	4614
X-RAY DIFFRACTION	r_mcangle_it	1.844	2	18683
X-RAY DIFFRACTION	r_scbond_it	2.871	3	7346
X-RAY DIFFRACTION	r_scangle_it	4.451	4.5	6951
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	0.394	458	-
R_work	0.354	30933	-
obs	-	-	98.4 %

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	0.3264	0.0537	0.1456	0.2972	0.0548	0.0826	0.003	-0.0286	0.0009	0.015	0.0298	-0.0621	0.0157	-0.0243	-0.0329	0.091	0.0016	0.0167	0.1146	-0.0169	0.1015	17.655	46.261	128.183
2	0.6315	-0.0575	-0.1603	0.3358	0.159	0.3684	-0.0574	-0.0338	0.0433	0.0589	0.06	-0.1181	-0.0033	0.0622	-0.0026	0.0671	-0.0022	-0.0142	0.0869	-0.027	0.1389	35.941	53.805	133.944
3	0.896	-0.029	0.0374	1.1117	0.2862	1.0867	-0.0399	-0.0693	0.1104	0.0041	-0.0115	0.1459	-0.1296	-0.1759	0.0514	0.076	0.0368	0.0076	0.1086	-0.0573	0.1472	10.683	62.348	133.997
4	1.6056	-0.6019	0.3336	1.5622	0.3828	0.9209	0.0517	0.0397	-0.2083	0.057	0.1491	-0.2659	0.152	0.1914	-0.2009	0.0377	0.0054	-0.0044	0.1199	-0.078	0.2094	49.965	36.808	118.595
5	0.3361	-0.0647	-0.0934	0.4138	0.1995	0.4545	-0.0084	0.0106	0.0852	-0.0054	0.0329	-0.0408	-0.0657	0.0098	-0.0246	0.065	-0.0055	0.0122	0.076	-0.0216	0.1198	26.692	59.266	123.68
6	0.1329	0.0527	-0.0434	0.2152	0.0159	0.1896	0.0259	0.0056	-0.0144	0.0158	0.0065	-0.0492	-0.021	0.0327	-0.0323	0.0625	0.0056	-0.0053	0.1013	0.0048	0.1068	27.443	23.867	129.594
7	0.6471	-0.1608	0.1961	0.3927	-0.118	0.3482	-0.0342	-0.0591	-0.04	0.063	0.0322	0.034	0.0129	-0.0542	0.002	0.0837	-0.0062	0.0207	0.1011	0.0152	0.0906	9.669	17.668	137.956
8	1.3262	-0.0552	0.0262	1.1722	-0.2793	1.1041	0.0288	0.003	-0.046	0.0148	-0.045	-0.2023	0.1285	0.1445	0.0162	0.0641	0.0266	-0.0171	0.1109	0.0325	0.1473	35.274	8.823	137.803
9	0.9981	-0.8354	-0.0071	1.1745	-0.1136	0.4141	0.0229	-0.0137	0.0681	-0.0316	0.0366	0.013	-0.0491	-0.0753	-0.0594	0.0846	-0.0034	0.0075	0.1185	0.0206	0.0909	-3.941	31.19	120.691
10	0.3487	-0.0654	0.2208	0.3384	-0.172	0.5674	0.0431	0.0113	-0.0917	-0.0091	-0.0033	-0.0294	0.0667	0.0468	-0.0398	0.0673	0.0029	-0.0013	0.0868	0.0028	0.0994	19.366	8.592	129
11	0.1642	-0.0017	0.1521	0.267	0.0796	0.1702	0.0112	0.0508	-0.0114	-0.1973	0.0198	-0.0529	-0.0493	0.0676	-0.031	0.1775	-0.0161	0.0219	0.1014	0.0011	0.03	9.728	37.121	80.514
12	0.235	-0.1593	0.193	0.5419	-0.1983	1.0956	0.0731	0.0419	-0.0758	-0.2405	-0.0342	0.0737	0.1192	-0.022	-0.0389	0.1778	-0.0131	-0.0343	0.0712	-0.0263	0.0291	0.42	19.517	74.892
13	0.335	-0.0799	0.1637	0.9864	-0.0061	0.7886	-0.0329	0.0562	0.0078	-0.1444	0.0359	-0.0778	-0.0249	-0.0169	-0.0029	0.2192	-0.0252	0.0085	0.2005	-0.0229	0.1292	5.012	23.687	82.739
14	2.0861	-1.196	0.539	1.175	-0.0642	0.656	0.0689	0.1015	-0.096	-0.2018	-0.0216	-0.0564	0.08	0.0924	-0.0473	0.1574	-0.008	0.0141	0.1128	-0.0175	0.0573	13.556	10.405	90.318
15	0.1387	-0.1229	0.2346	0.404	-0.01	0.7717	-0.0035	0.0152	-0.0099	-0.1485	0.0121	0.057	-0.0628	-0.0998	-0.0087	0.1296	-0.0081	-0.0334	0.1136	0.0068	0.0401	-4.381	29.797	84.228
16	0.4223	0.1223	-0.1011	0.3639	-0.1347	0.2949	0.0063	0.1159	-0.0554	-0.2115	0.0212	-0.127	0.0403	0.0582	-0.0275	0.1647	0.0041	0.087	0.1357	-0.0641	0.0816	30.835	25.306	80.555
17	0.5911	-0.198	-0.0353	1.0317	0.1343	0.7635	0.0703	0.2851	0.0123	-0.4295	-0.1021	-0.2202	-0.0581	0.1302	0.0319	0.2449	-0.0139	0.1448	0.2501	-0.0185	0.0954	39.347	38.944	70.831
18	2.0404	-0.2429	0.1104	1.0583	0.1466	1.6526	0.0459	0.1663	-0.3119	-0.2484	-0.0571	-0.3363	0.2716	0.3134	0.0111	0.2198	0.0588	0.1844	0.2203	-0.0817	0.3008	48.002	17.458	76.204
19	1.4317	-0.7089	0.1888	1.3535	-0.0429	0.5635	-0.0886	0.1928	0.1049	-0.1605	0.0543	-0.0216	-0.175	0.0241	0.0344	0.1833	-0.0479	0.0513	0.1236	0.0323	0.0667	26.139	58.464	87.286
20	0.4149	-0.2793	-0.1001	1.0416	0.3794	0.9489	0.0053	0.1502	-0.0185	-0.2031	0.0292	-0.3019	0.0432	0.2372	-0.0345	0.1158	-0.0021	0.1368	0.196	-0.0443	0.1771	46.985	31.34	81.045

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	43 - 159
2	X-RAY DIFFRACTION	2	A	160 - 293
3	X-RAY DIFFRACTION	3	A	294 - 356
4	X-RAY DIFFRACTION	4	A	357 - 461
5	X-RAY DIFFRACTION	5	A	462 - 618
6	X-RAY DIFFRACTION	6	B	43 - 159
7	X-RAY DIFFRACTION	7	B	160 - 293
8	X-RAY DIFFRACTION	8	B	294 - 354
9	X-RAY DIFFRACTION	9	B	355 - 474
10	X-RAY DIFFRACTION	10	B	475 - 618
11	X-RAY DIFFRACTION	11	C	45 - 159
12	X-RAY DIFFRACTION	12	C	160 - 293
13	X-RAY DIFFRACTION	13	C	294 - 410
14	X-RAY DIFFRACTION	14	C	411 - 461
15	X-RAY DIFFRACTION	15	C	462 - 619
16	X-RAY DIFFRACTION	16	D	45 - 160
17	X-RAY DIFFRACTION	17	D	161 - 307
18	X-RAY DIFFRACTION	18	D	308 - 358
19	X-RAY DIFFRACTION	19	D	359 - 474
20	X-RAY DIFFRACTION	20	D	475 - 618

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