PDB-4moe: Pyranose 2-oxidase H450G mutant with 3-fluorinated glucose

ID or keywords:

Entry

Database: PDB / ID: 4moe

Title

Pyranose 2-oxidase H450G mutant with 3-fluorinated glucose

Components

Pyranose 2-oxidase

Keywords

OXIDOREDUCTASE / GMC OXIDOREDUCTASE / PHBH FOLD / HOMOTETRAMER / FAD-BINDING / SUBSTRATE COMPLEX / FLAVINYLATION / INTRACELLULAR

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 /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Tan, T.C. / Spadiut, O. / Gandini, R. / Haltrich, D. / Divne, C.

Citation

Journal: Plos One / Year: 2014
Title: Structural Basis for Binding of Fluorinated Glucose and Galactose to Trametes multicolor Pyranose 2-Oxidase Variants with Improved Galactose Conversion.
Authors: Tan, T.C. / Spadiut, O. / Gandini, R. / Haltrich, D. / Divne, C.

History

Deposition	Sep 12, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 5, 2014	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	Jul 29, 2020	Group: Data collection / Database references / Derived calculations Category: chem_comp / pdbx_chem_comp_identifier ...chem_comp / pdbx_chem_comp_identifier / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen Item: _chem_comp.type / _struct_conn.pdbx_dist_value ..._chem_comp.type / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3	Nov 20, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4moe.cif.gz	909.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4moe.ent.gz	758.3 KB	Display	PDB format
PDBx/mmJSON format	4moe.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4moe_validation.pdf.gz	2.2 MB	Display	wwPDB validaton report
Full document	4moe_full_validation.pdf.gz	2.2 MB	Display
Data in XML	4moe_validation.xml.gz	110 KB	Display
Data in CIF	4moe_validation.cif.gz	145.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mo/4moe ftp://data.pdbj.org/pub/pdb/validation_reports/mo/4moe	HTTPS FTP

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Related structure data

Related structure data	4mofC 4mogC 4mohC 4moiC 4mojC 4mokC 4molC 4momC 4mooC 4mopC 4moqC 4morC 4mosC 1tt0 2igo 3pl8 C: citing same article (ref.)
Similar structure data	3k4m-1 1tzl-1 3lsh-d 4mom-d 1tt0-d 3lsi-1 4mok-d 1tzl-2 2ign-1 3k4n-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

289 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)	100.068, 102.742, 137.692
Angle α, β, γ (deg.)	90.00, 90.80, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein

Pyranose 2-oxidase / Pyranose oxidase

Mass: 70472.961 Da / Num. of mol.: 4 / Mutation: H450G
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

#3: Sugar

ChemComp-G3F / 3-deoxy-3-fluoro-beta-D-glucopyranose / 3-deoxy-3-fluoro-beta-D-glucose / 3-deoxy-3-fluoro-D-glucose / 3-deoxy-3-fluoro-glucose

Type: D-saccharide, beta linking / Mass: 182.147 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₁₁FO₅

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Non-polymers , 4 types, 1129 molecules

#2: Chemical	ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE Mass: 787.566 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₇H₃₅N₉O₁₅P₂
#4: Chemical	ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 Mass: 546.646 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₄H₅₀O₁₃ / Comment: precipitant*YM
#5: Chemical	ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID Mass: 195.237 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₆H₁₃NO₄S / Comment: pH buffer*YM
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1116 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has protein modification	Y
Sequence details	THIS IS A CLONING ARTIFACT

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.51 Å³/Da / Density % sol: 51.01 %
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

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.0379 Å
Detector	Type: MAR CCD 165 mm / Detector: CCD / Date: Apr 4, 2009 / Details: Multilayer mirror
Radiation	Monochromator: Bent Si(111) crystal, horisontally focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0379 Å / Relative weight: 1
Reflection	Resolution: 1.9→57.19 Å / Num. all: 214367 / Num. obs: 214367 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Net I/σ(I): 12.4
Reflection shell	Resolution: 1.9→2 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.5 / % possible all: 98.4

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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 / Resolution: 2→50 Å / Cor.coef. F_o:F_c: 0.942 / Cor.coef. F_o:F_c free: 0.903 / SU B: 8.047 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.242	3290	1.8 %	RANDOM
R_work	0.195	-	-	-
obs	0.196	180555	97.7 %	-
all	-	180555	-	-

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: 25.91 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.48 Å²	0 Å²	-0.42 Å²
2-	-	-0.33 Å²	0 Å²
3-	-	-	1.8 Å²

Refinement step

Cycle: LAST / Resolution: 2→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18119	0	376	1116	19611

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.02	18988
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	12828
X-RAY DIFFRACTION	r_angle_refined_deg	2.012	1.97	25814
X-RAY DIFFRACTION	r_angle_other_deg	1.034	3	31266
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.024	5	2297
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.966	24.497	894
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.675	15	3025
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.274	15	108
X-RAY DIFFRACTION	r_chiral_restr	0.15	0.2	2818
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.021	20907
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3805
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2→2.11 Å / Total num. of bins used: 10

	R_factor	Num. reflection	% reflection
R_free	0.287	481	-
R_work	0.242	25975	-
obs	-	-	98.91 %

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	0.2328	0.033	0.1927	0.3722	0.1139	0.4129	0.0126	-0.0181	-0.0073	0.0106	0.0105	-0.0492	0.0381	-0.0095	-0.0231	0.1151	-0.0073	0.0098	0.1277	-0.0019	0.1432	18.0752	46.2059	128.2441
2	0.7152	-0.0947	-0.26	0.3772	0.1938	0.3985	-0.0214	0.0019	0.0095	0.0264	0.0466	-0.1249	0.0008	0.06	-0.0252	0.0963	-0.0064	-0.0268	0.1111	-0.0224	0.1558	36.1791	53.784	133.8703
3	1.1031	-0.2475	-0.3214	1.4742	0.1534	1.69	0.0441	0.0103	0.0909	-0.0423	0.017	0.1471	-0.1603	-0.2147	-0.0611	0.1041	0.0002	-0.0102	0.1398	-0.0325	0.1777	11.4456	62.1192	133.7233
4	1.112	-0.1651	0.3038	1.1299	0.2314	0.8112	0.0495	0.0563	-0.2628	0.0654	0.1112	-0.2232	0.1518	0.19	-0.1607	0.0821	0.0154	-0.0167	0.1314	-0.0621	0.228	50.2009	36.0373	117.7939
5	0.5149	-0.1365	-0.219	0.412	0.2499	0.5444	0.0139	0.0132	0.0442	-0.0249	0.0202	-0.0327	-0.0669	-0.0066	-0.0342	0.1048	-0.0054	0.0006	0.1004	-0.0058	0.1387	26.0607	60.5889	124.2229
6	0.2467	0.0589	-0.1738	0.3539	-0.1	0.5754	0.0241	-0.0164	-0.0081	-0.0025	0.0093	-0.0564	-0.0098	0.0649	-0.0334	0.0984	-0.001	-0.0224	0.1232	-0.0084	0.1417	27.8967	23.8199	129.609
7	0.768	-0.1299	0.1194	0.3249	-0.1148	0.3353	-0.0253	-0.0483	-0.0789	0.0517	0.0193	0.0405	0.0186	-0.0484	0.006	0.1208	-0.0025	0.0036	0.1189	0.014	0.124	10.0379	17.3958	137.9018
8	1.4705	0.1839	0.2896	1.4214	-0.1747	1.6419	0.0437	0.0112	-0.0927	-0.0233	-0.0085	-0.2453	0.1786	0.1801	-0.0352	0.096	0.029	-0.0225	0.1245	0.0271	0.1941	35.3524	8.5453	137.2263
9	0.9221	-0.6072	-0.1566	1.0329	0.0499	0.5106	0.0168	0.0106	0.0635	-0.0131	0.0296	0.0552	-0.0689	-0.0661	-0.0464	0.113	-0.0069	-0.003	0.1294	0.0096	0.1264	-4.0897	31.7751	120.316
10	0.4109	-0.1337	0.1819	0.3337	-0.194	0.4298	0.0226	-0.0034	-0.0777	-0.0236	-0.0029	-0.0534	0.0535	0.0375	-0.0196	0.1089	0.0052	-0.0102	0.1016	0.0019	0.1317	19.9773	8.549	128.8722
11	0.2269	0.1578	0.1726	0.3231	0.2347	0.2961	0.0093	0.0455	-0.0185	-0.1007	0.0383	-0.053	-0.0397	0.0615	-0.0476	0.1755	-0.0094	0.001	0.1361	0	0.0456	9.8611	37.1525	80.3256
12	0.2227	-0.0067	0.0955	0.6612	-0.2683	0.6963	0.0221	0.0499	-0.0444	-0.0608	-0.0085	0.0349	0.0598	-0.0232	-0.0136	0.1772	-0.0015	-0.0277	0.1348	-0.0283	0.049	0.7009	19.6875	74.7151
13	1.1729	-0.1138	-0.0854	1.2368	-0.1036	1.9552	0.0045	0.0251	0.191	-0.0993	0.0167	0.0739	-0.3291	-0.186	-0.0212	0.2071	0.0205	-0.0481	0.1128	0.0127	0.0715	-5.5837	45.0026	73.6061
14	0.6778	-0.0533	0.0398	1.5165	0.1227	0.9349	-0.0295	0.1051	-0.2082	-0.0473	0.0832	-0.3206	0.3074	0.2319	-0.0537	0.1588	0.0376	0.0048	0.1225	-0.0566	0.1432	20.8795	-1.5349	92.6413
15	0.2155	-0.1533	0.2265	0.5547	-0.1896	0.6662	0.0093	0.0499	0.01	-0.0655	0.0139	0.0006	-0.0297	-0.0206	-0.0232	0.1483	-0.0024	-0.0099	0.1489	-0.0023	0.0731	-2.1398	27.3607	85.2197
16	0.4934	0.0557	-0.0153	0.4206	-0.0697	0.4728	0.0049	0.2039	-0.0141	-0.1488	0.0588	-0.1414	-0.0617	0.1106	-0.0637	0.125	-0.0211	0.0772	0.1796	-0.0697	0.083	34.9826	28.9579	78.8721
17	0.8687	-0.1584	0.1832	0.9765	0.3411	0.973	0.0219	0.3708	-0.0958	-0.3854	-0.018	-0.064	-0.1808	0.1091	-0.0038	0.2125	-0.0329	0.0774	0.2449	-0.0552	0.0621	37.0566	37.0743	69.0685
18	2.2198	0.7766	-0.9397	1.1685	1.1127	3.0407	-0.0634	-0.0343	-0.595	-0.1101	0.2604	-0.5914	0.0686	0.3719	-0.197	0.1098	-0.0181	0.13	0.1887	-0.1453	0.3979	49.696	18.7109	78.4036
19	1.1085	-0.5046	0.3439	1.1521	-0.1006	0.5528	-0.0783	0.132	0.0404	-0.1141	0.0506	0.0166	-0.1463	-0.032	0.0277	0.1943	-0.0387	0.0351	0.1702	0.0197	0.0796	25.7215	58.9781	87.3958
20	0.4934	-0.1899	0.0032	0.5424	0.3723	0.5588	-0.0096	0.2126	-0.0998	-0.1236	0.0909	-0.1869	0.0098	0.1918	-0.0814	0.0838	-0.0232	0.1067	0.2033	-0.0926	0.1677	46.9933	31.8042	80.8273

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	43 - 158
2	X-RAY DIFFRACTION	2	A	159 - 293
3	X-RAY DIFFRACTION	3	A	294 - 358
4	X-RAY DIFFRACTION	4	A	359 - 469
5	X-RAY DIFFRACTION	5	A	470 - 618
6	X-RAY DIFFRACTION	6	B	43 - 160
7	X-RAY DIFFRACTION	7	B	161 - 293
8	X-RAY DIFFRACTION	8	B	294 - 356
9	X-RAY DIFFRACTION	9	B	357 - 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 - 358
14	X-RAY DIFFRACTION	14	C	359 - 428
15	X-RAY DIFFRACTION	15	C	429 - 618
16	X-RAY DIFFRACTION	16	D	45 - 192
17	X-RAY DIFFRACTION	17	D	193 - 314
18	X-RAY DIFFRACTION	18	D	315 - 358
19	X-RAY DIFFRACTION	19	D	359 - 472
20	X-RAY DIFFRACTION	20	D	473 - 618

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Non-polymers , 4 types, 1129 molecules

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Details

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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Yorodumi