PDB-3k4c: Pyranose 2-oxidase H167A/T169G mutant

ID or keywords:

Entry

Database: PDB / ID: 3k4c

Title

Pyranose 2-oxidase H167A/T169G mutant

Components

Pyranose 2-oxidase

Keywords

OXIDOREDUCTASE / GMC OXIDOREDUCTASE / H167A/T169G MUTANT / ROSSMANN FOLD / PHBH FOLD / HOMOTETRAMER / 8-ALPHA-(N3) HISTIDYL FLAVINYLATION

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: 1.7 Å

Authors

Divne, C. / Tan, T.C.

Citation

Journal: J.Biol.Chem. / Year: 2010
Title: A conserved active-site threonine is important for both sugar and flavin oxidations of pyranose 2-oxidase.
Authors: Pitsawong, W. / Sucharitakul, J. / Prongjit, M. / Tan, T.C. / Spadiut, O. / Haltrich, D. / Divne, C. / Chaiyen, P.

History

Deposition	Oct 5, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 2, 2010	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 1, 2017	Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site / _software.name
Revision 1.4	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 1.5	Sep 6, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3k4c.cif.gz	504.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3k4c.ent.gz	410.1 KB	Display	PDB format
PDBx/mmJSON format	3k4c.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3k4c_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	3k4c_full_validation.pdf.gz	1.5 MB	Display
Data in XML	3k4c_validation.xml.gz	106.1 KB	Display
Data in CIF	3k4c_validation.cif.gz	153.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/k4/3k4c ftp://data.pdbj.org/pub/pdb/validation_reports/k4/3k4c	HTTPS FTP

-
Related structure data

Related structure data	3k4bC 1tt0S 2igk 2igm 2ign 2igo 3bg6 S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3lsk-d 4mop-d 4mof-1 3k4l-1 4mor-d 4mol-d 4moo-1 2igk-2 2ign-2 2igk-1 3k4b-1 3lsm-1 4mog-1 3bg7-1 1tzl-2 3k4n-1 2f6c-1 3fdy-1 4mok-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
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

282 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)	100.206, 102.964, 137.122
Angle α, β, γ (deg.)	90.00, 90.82, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Pyranose 2-oxidase / Pyranose oxidase Mass: 69302.664 Da / Num. of mol.: 4 / Mutation: H167A, T169G 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.: 4 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Comment: FAD*YM
#3: Chemical	ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 Mass: 238.278 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₂₂O₆ / Comment: precipitant*YM
#4: Chemical	ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₃NO₄S / Comment: pH buffer*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1900 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.55 Å³/Da / Density % sol: 51.79 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: 0.1M MES, 50MM MGCL2, 10% (W/V)% MONOMETHYLETHER PEG 2000, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.0379 Å
Detector	Type: MARRESEARCH / Detector: CCD / Date: Apr 6, 2009 / Details: MIRRORS
Radiation	Monochromator: BENT SI (111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0379 Å / Relative weight: 1
Reflection	Resolution: 1.7→30 Å / Num. all: 295544 / Num. obs: 295544 / % possible obs: 96.8 % / Redundancy: 3 % / R_sym value: 0.067 / Net I/σ(I): 12.3
Reflection shell	Resolution: 1.7→1.8 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 47143 / R_sym value: 0.76 / % possible all: 98.3

-
Processing

Software

Name	Version	Classification
MAR345		data collection
REFMAC	5.5	refinement
XDS		data reduction
XSCALE		data scaling
REFMAC	5.5	phasing

Refinement

Method to determine structure:

FOURIER SYNTHESIS
Starting model: pdb entry 1TT0

1tt0

Resolution: 1.7→29.3 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.943 / SU B: 4.885 / SU ML: 0.075 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21631	3027	1 %	RANDOM
R_work	0.18019	-	-	-
all	0.18056	292517	-	-
obs	0.18056	292517	96.83 %	-

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: 12.274 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.87 Å²	0 Å²	-0.44 Å²
2-	-	-0.03 Å²	0 Å²
3-	-	-	0.89 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→29.3 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18111	0	294	1900	20305

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.024	0.022	18882
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	16430
X-RAY DIFFRACTION	r_angle_refined_deg	2.071	1.963	25660
X-RAY DIFFRACTION	r_angle_other_deg	3.275	3	38387
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.997	5	2297
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.946	24.497	894
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.216	15	3021
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.744	15	108
X-RAY DIFFRACTION	r_chiral_restr	0.187	0.2	2784
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.021	20915
X-RAY DIFFRACTION	r_gen_planes_other	0	0.02	3761
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	1.253	1.5	11494
X-RAY DIFFRACTION	r_mcbond_other	0.441	1.5	4618
X-RAY DIFFRACTION	r_mcangle_it	2.039	2	18671
X-RAY DIFFRACTION	r_scbond_it	3.101	3	7388
X-RAY DIFFRACTION	r_scangle_it	4.756	4.5	6989
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.7→1.792 Å / Total num. of bins used: 10

	R_factor	Num. reflection	% reflection
R_free	0.302	432	-
R_work	0.258	43138	-
obs	-	-	98.31 %

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	0.1744	0.0769	0.1032	0.353	0.0659	0.0778	0.0204	-0.0053	0.0068	0.0025	-0.0008	-0.028	0.0348	-0.0177	-0.0196	0.1074	-0.0032	0.0175	0.1025	-0.0065	0.0844	18.042	46.227	127.636
2	0.5025	-0.0646	-0.1027	0.2728	0.1404	0.3626	-0.0369	-0.0214	0.0215	0.0494	0.0512	-0.0931	-0.0042	0.0578	-0.0143	0.0869	-0.0065	-0.0039	0.0784	-0.0219	0.1146	36.351	53.935	133.127
3	0.6094	-0.1536	-0.0871	0.7978	0.119	1.1599	0.0046	0.0002	0.0594	-0.0154	-0.0032	0.144	-0.0812	-0.1357	-0.0014	0.0876	0.0154	0.0099	0.0849	-0.0239	0.1234	11.434	62.115	133.143
4	0.7758	-0.8541	0.1839	2.5358	0.2077	0.6296	0.0128	0.0521	-0.0454	0.1671	0.1052	-0.3353	0.0988	0.1102	-0.1179	0.0648	0.0001	-0.0188	0.0877	-0.0556	0.1539	49.318	37.533	116.904
5	0.375	-0.0013	-0.1267	0.3379	0.1509	0.3739	0.0085	0.0256	0.0824	-0.0171	0.0169	-0.0116	-0.0583	-0.0122	-0.0254	0.0853	0.0002	0.0172	0.0655	-0.0077	0.0888	25.358	61.206	124.131
6	0.2355	0.0336	-0.092	0.2341	-0.0252	0.3802	0.0289	-0.0105	-0.031	0.0027	0.016	-0.0202	-0.0146	0.0452	-0.0449	0.091	-0.0026	-0.0036	0.0861	-0.0044	0.0838	27.842	23.874	128.858
7	0.6328	-0.1097	0.2184	0.2616	-0.1256	0.3453	-0.0014	-0.0631	-0.0566	0.0434	0.0226	0.0227	0.0189	-0.0579	-0.0213	0.0984	-0.004	0.0203	0.0875	0.0135	0.0778	10.384	17.58	137.179
8	0.9458	-0.1117	0.2537	1.0704	-0.093	0.9854	0.0369	-0.0088	-0.057	0.0076	-0.0397	-0.1977	0.1017	0.1191	0.0028	0.086	0.0195	-0.0004	0.092	0.0237	0.1273	35.065	8.585	136.327
9	0.7896	-0.8337	-0.0736	1.4582	-0.1448	0.616	0.0338	0.018	0.0405	-0.0092	0.0577	0.0837	-0.0723	-0.0761	-0.0916	0.084	-0.0001	0.0162	0.0943	0.0284	0.0888	-4.275	31.911	119.976
10	0.4446	-0.0921	0.3092	0.2833	-0.1698	0.4646	0.0512	0.0057	-0.095	-0.0049	0.002	-0.0219	0.0483	0.014	-0.0531	0.0892	0.0038	-0.0003	0.0678	-0.0001	0.0781	19.921	8.615	128.251
11	0.2048	0.1132	0.238	0.2562	0.2388	0.3377	-0.0211	0.0836	-0.0069	-0.1101	0.0451	-0.0315	-0.0826	0.1075	-0.024	0.1438	-0.0187	0.0215	0.1255	0.0047	0.0091	9.799	37.185	79.951
12	0.2683	-0.0565	0.1333	0.5239	-0.1091	0.7071	0.0264	0.067	-0.0497	-0.129	0.0108	0.0453	0.0692	0.0083	-0.0372	0.1226	-0.011	-0.0113	0.111	-0.0229	0.0141	0.661	19.725	74.408
13	0.7397	-0.0529	0.0566	0.8066	-0.0338	2.0159	-0.0173	0.0288	0.1513	-0.1084	0.0329	0.0155	-0.2788	-0.1278	-0.0156	0.171	0.0083	-0.029	0.0852	0.0164	0.0391	-5.64	44.619	73.585
14	0.7351	-0.0212	0.196	1.0311	0.093	0.7931	0.0171	0.1228	-0.0697	-0.0542	0.0457	-0.1944	0.1593	0.1212	-0.0627	0.1566	0.0197	-0.0026	0.1347	-0.0481	0.0671	16.208	5.232	91.761
15	0.1138	-0.0304	0.0871	0.2512	-0.0978	0.5671	0.0057	0.0314	0.0147	-0.065	0.0404	0.0492	-0.0474	-0.0557	-0.0461	0.1228	0.0001	-0.0191	0.1164	0.0105	0.0436	-5.946	31.193	82.749
16	2.7443	0.6553	1.4186	1.6021	-0.7654	3.5698	-0.0257	1.1744	-0.428	-0.3617	0.368	-0.1185	0.244	0.4777	-0.3424	0.2411	-0.1496	0.1248	0.8973	-0.3313	0.1765	36.242	27.399	61.265
17	0.4598	0.3301	0.0078	0.393	0.0887	0.0502	-0.0278	0.1248	-0.0596	-0.0561	0.0875	-0.1314	-0.0261	0.0198	-0.0597	0.1045	-0.0008	0.047	0.1643	-0.0566	0.0803	26.778	24.687	89.857
18	1.2599	0.1008	0.2032	0.8789	0.3667	0.5358	-0.0715	0.6443	-0.1637	-0.2117	0.1893	-0.2288	-0.1095	0.267	-0.1178	0.1508	-0.0827	0.1191	0.4457	-0.1317	0.1108	40.829	34.623	72.994
19	2.1033	-1.5151	0.7082	1.7478	-0.1263	1.0639	-0.1182	0.2733	0.0948	-0.1918	0.0291	-0.0057	-0.2596	0.0341	0.0891	0.2275	-0.0714	0.0415	0.1877	0.0494	0.0721	24.677	61.504	85.405
20	1.1928	0.1843	0.3677	0.4566	0.2281	0.4221	-0.0892	0.512	-0.1394	-0.1155	0.2133	-0.2272	-0.0376	0.2796	-0.1241	0.0945	-0.0584	0.0969	0.336	-0.126	0.1389	45.293	33.605	80.994

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 - 358
4	X-RAY DIFFRACTION	4	A	359 - 476
5	X-RAY DIFFRACTION	5	A	477 - 618
6	X-RAY DIFFRACTION	6	B	43 - 157
7	X-RAY DIFFRACTION	7	B	158 - 293
8	X-RAY DIFFRACTION	8	B	294 - 357
9	X-RAY DIFFRACTION	9	B	358 - 474
10	X-RAY DIFFRACTION	10	B	475 - 618
11	X-RAY DIFFRACTION	11	C	45 - 158
12	X-RAY DIFFRACTION	12	C	159 - 293
13	X-RAY DIFFRACTION	13	C	294 - 359
14	X-RAY DIFFRACTION	14	C	360 - 473
15	X-RAY DIFFRACTION	15	C	474 - 619
16	X-RAY DIFFRACTION	16	D	45 - 85
17	X-RAY DIFFRACTION	17	D	86 - 149
18	X-RAY DIFFRACTION	18	D	150 - 370
19	X-RAY DIFFRACTION	19	D	371 - 461
20	X-RAY DIFFRACTION	20	D	462 - 618

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi