PDB-4mol: Pyranose 2-oxidase H167A mutant with 2-fluorinated galactose

ID or keywords:

Entry

Database: PDB / ID: 4mol

Title

Pyranose 2-oxidase H167A mutant with 2-fluorinated galactose

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	Jul 29, 2020	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4mol.cif.gz	925.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4mol.ent.gz	767.1 KB	Display	PDB format
PDBx/mmJSON format	4mol.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4mol_validation.pdf.gz	2.2 MB	Display	wwPDB validaton report
Full document	4mol_full_validation.pdf.gz	2.3 MB	Display
Data in XML	4mol_validation.xml.gz	100.7 KB	Display
Data in CIF	4mol_validation.cif.gz	146.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mo/4mol ftp://data.pdbj.org/pub/pdb/validation_reports/mo/4mol	HTTPS FTP

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Related structure data

Related structure data	4moeC 4mofC 4mogC 4mohC 4moiC 4mojC 4mokC 4momC 4mooC 4mopC 4moqC 4morC 4mosC 1tt0 2igo 3pl8 C: citing same article (ref.)
Similar structure data	3k4c-d 3lsk-d 4mop-d 2f6c-1 3pl8-1 4mor-d 4mof-1 4moo-1 3k4l-1 4mog-1 4moh-1 2igk-2 4mok-d 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

288 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)	100.291, 102.476, 137.423
Angle α, β, γ (deg.)	90.00, 91.02, 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: 70486.984 Da / Num. of mol.: 4 / Mutation: H167A
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-2FG / 2-deoxy-2-fluoro-beta-D-galactopyranose / 2-FLUORO-2-DEOXY-BETA-D-GALACTOPYRANOSE / 2-deoxy-2-fluoro-beta-D-galactose / 2-deoxy-2-fluoro-D-galactose / 2-deoxy-2-fluoro-galactose

Type: D-saccharide, beta linking / Mass: 182.147 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C₆H₁₁FO₅

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Non-polymers , 4 types, 1776 molecules

#2: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Comment: FAD*YM
#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.: 2 / Source method: obtained synthetically / Formula: C₆H₁₃NO₄S / Comment: pH buffer*YM
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1766 / 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: 2.5 Å³/Da / Density % sol: 50.88 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: 0.1 M MES, 50 mM 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: Diamond / Beamline: I24 / Wavelength: 0.9191 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2013 Details: Oxford Danfysik/SESO two stage demagnification using two K-B pairs of bimorph type mirrors
Radiation	Monochromator: ACCEL fixed-exit double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9191 Å / Relative weight: 1
Reflection	Resolution: 2→48.01 Å / Num. all: 184127 / Num. obs: 184127 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Net I/σ(I): 11.5
Reflection shell	Resolution: 2→2.1 Å / Redundancy: 7 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 24662 / % possible all: 97.2

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2→48.01 Å / Cor.coef. F_o:F_c: 0.946 / Cor.coef. F_o:F_c free: 0.925 / SU B: 6.381 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.168 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22166	1846	1 %	RANDOM
R_work	0.18601	-	-	-
all	0.18637	182281	-	-
obs	0.18637	182281	98.18 %	-

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: 34.93 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.82 Å²	0 Å²	-0.2 Å²
2-	-	-0.58 Å²	0 Å²
3-	-	-	1.39 Å²

Refinement step

Cycle: LAST / Resolution: 2→48.01 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18076	0	345	1766	20187

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.019	0.02	18949
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	12812
X-RAY DIFFRACTION	r_angle_refined_deg	1.921	1.967	25761
X-RAY DIFFRACTION	r_angle_other_deg	1.004	3	31191
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.028	5	2303
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.621	24.41	898
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.675	15	3030
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.429	15	113
X-RAY DIFFRACTION	r_chiral_restr	0.15	0.2	2810
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.021	20931
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3818

LS refinement shell

Resolution: 2→2.108 Å / Total num. of bins used: 10

	R_factor	Num. reflection	% reflection
R_free	0.313	242	-
R_work	0.27	25785	-
obs	-	-	97.13 %

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	0.1808	-0.0212	-0.047	0.2175	0.0112	0.2595	0.0135	-0.0023	0.0035	0.0206	0.0084	0.0352	-0.0235	-0.0203	-0.0218	0.0498	0.0006	-0.0132	0.0548	-0.0005	0.075	-26.9326	22.9186	-60.4503
2	0.7676	0.1998	0.194	0.3347	0.1568	0.3447	-0.0166	0.0543	-0.0843	-0.011	0.03	-0.0476	0.035	0.0619	-0.0134	0.086	0.0075	0.0077	0.0811	-0.0204	0.0949	-10.2664	16.257	-69.1347
3	1.3637	-0.321	0.3562	1.0672	0.2558	1.5191	0.019	0.0077	-0.1234	-0.0109	0.0299	0.2112	0.1621	-0.1957	-0.0489	0.0605	-0.0234	-0.0152	0.0818	-0.0175	0.1393	-36.1314	8.0017	-68.2674
4	1.0505	0.9552	-0.07	1.4434	0.0433	0.5353	0.013	-0.0247	0.1131	0.0189	0.0334	0.0098	-0.0721	0.0641	-0.0464	0.0851	0.0154	-0.0134	0.1018	-0.0175	0.0916	4.3127	31.3266	-51.7678
5	0.3819	0.105	0.1493	0.3004	0.1704	0.4128	0.0242	0.009	-0.064	0.0097	0.0029	0.028	0.0608	-0.0242	-0.0271	0.0678	0.0069	-0.012	0.0585	-0.0006	0.0884	-19.07	9.7603	-58.6903
6	0.1083	-0.0683	0.1419	0.2613	-0.143	0.2002	0.0132	-0.0312	-0.0178	0.1318	0.0249	0.0621	-0.0137	-0.0351	-0.0381	0.1199	0.0056	0.0139	0.0656	-0.0001	0.0248	-11.0784	36.1611	-11.6502
7	0.2186	0.0792	0.1271	0.6261	0.1847	0.74	0.0278	-0.0391	-0.0426	0.1143	-0.0071	-0.04	0.0413	0.0578	-0.0207	0.1275	0.0142	-0.0261	0.072	0.0204	0.0242	-1.7741	18.5892	-5.8745
8	0.5616	0.1411	0.1387	1.032	0.3141	1.0968	-0.0031	-0.0628	0.0693	0.1065	0.0001	0.0384	-0.1127	0.0497	0.003	0.1852	0.0374	-0.0031	0.1787	0.0325	0.124	-3.4854	30.2922	-12.3253
9	1.4319	0.6137	-0.1809	1.1457	-0.1168	0.6448	-0.013	-0.0678	0.0213	0.0737	0.0279	0.1764	0.1141	-0.077	-0.015	0.1503	0.0097	-0.0158	0.0993	0.028	0.0588	-16.1795	4.199	-21.0668
10	0.1991	0.0839	0.1451	0.3732	-0.0142	0.519	0.0141	-0.0299	0.0137	0.1067	0.0104	-0.0487	-0.0613	0.0927	-0.0245	0.095	0.004	-0.0277	0.0793	-0.0026	0.0386	3.0928	28.8109	-15.4349
11	0.2634	-0.0441	0.0563	0.3462	0.0545	0.3189	0.002	-0.1608	0.0008	0.1611	0.0334	0.1117	-0.0345	-0.0914	-0.0354	0.0992	0.0205	0.0716	0.1267	0.0211	0.0532	-36.2765	34.9901	-6.8609
12	16.4581	-0.7228	-2.1848	1.6694	0.7352	0.5438	0.183	-0.086	-0.8109	0.5359	-0.2109	-0.0607	0.1711	-0.0827	0.0279	0.2357	-0.006	0.0438	0.0944	0.1154	0.1867	-42.833	10.9048	2.7875
13	1.6689	-0.1674	-0.0912	0.8812	-0.5857	2.3176	0.0064	-0.0657	-0.3111	0.079	0.0076	0.3364	0.2782	-0.2866	-0.014	0.0839	-0.0172	0.0876	0.109	0.0399	0.2301	-50.1878	18.2254	-8.2373
14	1.5308	0.8507	0.3295	1.2394	0.2322	0.6964	-0.0525	-0.058	0.0082	0.0997	0.0518	-0.0697	-0.1153	0.0516	0.0008	0.1422	0.0387	0.0264	0.113	-0.0164	0.062	-26.4349	58.532	-18.3907
15	0.3786	0.1781	-0.0137	0.599	-0.2869	0.5756	-0.0084	-0.1464	-0.0592	0.1386	0.0532	0.1882	0.0363	-0.159	-0.0449	0.0707	0.009	0.0808	0.1147	0.0549	0.1128	-47.8451	31.4163	-12.3025
16	0.7687	0.0364	0.1964	1.2091	-0.5108	0.789	-0.0287	0.0421	-0.0243	-0.0987	0.0174	-0.0421	0.0756	0.0558	0.0113	0.0722	0.0056	-0.0069	0.0641	-0.0137	0.0783	-25.7422	45.5549	-69.6339
17	0.2523	-0.0032	0.0748	0.2134	-0.0408	0.2496	-0.013	0.0222	0.0329	-0.0094	0.0263	0.0666	-0.0191	-0.0288	-0.0133	0.0664	-0.0016	-0.0068	0.0513	0.0082	0.0926	-30.151	50.982	-59.4968
18	1.1396	0.1148	-0.33	1.2457	-0.205	1.5783	0.0119	0.0067	0.0994	-0.0275	0.0253	-0.1963	-0.161	0.2303	-0.0372	0.0608	-0.0178	-0.0169	0.0846	0.0259	0.125	-12.3598	61.2843	-64.6279
19	1.1272	0.2381	0.3846	1.1872	-0.0485	0.7621	0.0417	-0.0665	-0.262	-0.0231	0.0723	0.1138	0.1123	-0.1376	-0.114	0.0598	-0.0068	-0.0008	0.103	0.0366	0.1615	-50.8585	35.4083	-48.9303
20	0.4354	0.0538	-0.1287	0.384	-0.1808	0.4549	-0.0049	0.0007	0.0749	-0.0004	0.0176	0.0206	-0.0587	0.0174	-0.0127	0.0678	0.0016	-0.0076	0.0498	0.0006	0.0933	-26.9363	59.8769	-55.218

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	46 - 174
2	X-RAY DIFFRACTION	2	A	175 - 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	46 - 159
7	X-RAY DIFFRACTION	7	B	160 - 293
8	X-RAY DIFFRACTION	8	B	294 - 390
9	X-RAY DIFFRACTION	9	B	391 - 461
10	X-RAY DIFFRACTION	10	B	462 - 618
11	X-RAY DIFFRACTION	11	C	46 - 282
12	X-RAY DIFFRACTION	12	C	283 - 310
13	X-RAY DIFFRACTION	13	C	311 - 359
14	X-RAY DIFFRACTION	14	C	360 - 470
15	X-RAY DIFFRACTION	15	C	471 - 618
16	X-RAY DIFFRACTION	16	D	46 - 113
17	X-RAY DIFFRACTION	17	D	114 - 293
18	X-RAY DIFFRACTION	18	D	294 - 358
19	X-RAY DIFFRACTION	19	D	359 - 470
20	X-RAY DIFFRACTION	20	D	471 - 618

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Experimental details

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