PDB-4moj: Pyranose 2-oxidase H450G/V546C double mutant with 2-fluorinated g...

ID or keywords:

Entry

Database: PDB / ID: 4moj

Title

Pyranose 2-oxidase H450G/V546C double mutant with 2-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 / 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_leaving_atom_flag / _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 / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4moj.cif.gz	922.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4moj.ent.gz	769.8 KB	Display	PDB format
PDBx/mmJSON format	4moj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4moj_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	4moj_full_validation.pdf.gz	1.5 MB	Display
Data in XML	4moj_validation.xml.gz	120.3 KB	Display
Data in CIF	4moj_validation.cif.gz	164.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mo/4moj ftp://data.pdbj.org/pub/pdb/validation_reports/mo/4moj	HTTPS FTP

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Related structure data

Related structure data	4moeC 4mofC 4mogC 4mohC 4moiC 4mokC 4molC 4momC 4mooC 4mopC 4moqC 4morC 4mosC 1tt0 2igo 3pl8 C: citing same article (ref.)
Similar structure data	2igo-1 2ign-1 3lsh-d 2igo-2 3bg6-1 1tzl-1 3k4m-1 2ign-2 3k4k-1 3fdy-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)	100.079, 102.520, 137.339
Angle α, β, γ (deg.)	90.00, 90.92, 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: 70476.969 Da / Num. of mol.: 4 / Mutation: H450G, V546C
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-G2F / 2-deoxy-2-fluoro-alpha-D-glucopyranose / 2-deoxy-2-fluoro-alpha-D-glucose / 2-deoxy-2-fluoro-D-glucose / 2-deoxy-2-fluoro-glucose

Type: D-saccharide, alpha 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, 1938 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-1PE / PENTAETHYLENE GLYCOL / PEG400 Mass: 238.278 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₂₂O₆ / Comment: precipitant*YM
#5: Chemical	ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₁₃NO₄S / Comment: pH buffer*YM
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1926 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has protein modification	Y

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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: 50.78 %
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: MAX II / Beamline: I911-2 / Wavelength: 1.0379 Å
Detector	Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 27, 2008 / 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: 2→57.05 Å / Num. all: 186674 / Num. obs: 186674 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Net I/σ(I): 12
Reflection shell	Resolution: 2→2.1 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 25332 / % possible all: 99.7

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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

Resolution: 2→50 Å / Cor.coef. F_o:F_c: 0.954 / Cor.coef. F_o:F_c free: 0.93 / SU B: 7.686 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.156 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.222	3748	2 %	RANDOM
R_work	0.172	-	-	-
obs	0.173	183034	99.8 %	-

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: 29.9 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.08 Å²	0 Å²	-0.5 Å²
2-	-	-0.03 Å²	0 Å²
3-	-	-	1.09 Å²

Refinement step

Cycle: LAST / Resolution: 2→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18115	0	368	1926	20409

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.019	0.02	18971
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	12818
X-RAY DIFFRACTION	r_angle_refined_deg	1.987	1.967	25789
X-RAY DIFFRACTION	r_angle_other_deg	1.033	3	31205
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.14	5	2299
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.619	24.503	895
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.851	15	3027
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.352	15	108
X-RAY DIFFRACTION	r_chiral_restr	0.148	0.2	2811
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.021	20942
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3806
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	0.278	560	-
R_work	0.242	26072	-
obs	-	-	99.73 %

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	0.2332	0.0682	0.1989	0.3332	0.1671	0.3947	0.0052	-0.0245	0.0253	0.0294	0.0021	-0.017	0.0273	-0.0225	-0.0073	0.0721	0.0006	0.0112	0.0712	-0.0025	0.0901	18.0452	46.1464	128.1035
2	0.5943	-0.099	-0.1477	0.2635	0.1227	0.3278	-0.0251	-0.0047	0.0282	0.0222	0.0259	-0.0666	-0.004	0.0371	-0.0008	0.064	-0.0026	-0.0217	0.0429	-0.017	0.1037	36.5313	54.0369	133.4175
3	0.9581	-0.1883	-0.1193	0.9838	0.4508	0.969	0.0112	0.0019	0.1045	-0.0118	0.0044	0.1618	-0.1428	-0.195	-0.0156	0.0664	0.0237	0.0003	0.081	-0.0145	0.1258	11.2217	62.0297	133.3159
4	1.1359	-0.1816	0.4363	1.1187	0.0191	0.7008	0.0563	0.0558	-0.287	0.0402	0.0824	-0.1339	0.1217	0.1289	-0.1387	0.0488	0.0011	-0.0101	0.0753	-0.0392	0.1508	50.5183	36.1563	117.8353
5	0.4068	-0.1006	-0.0918	0.3056	0.1968	0.3719	0.0017	0.018	0.0769	-0.0033	0.0094	-0.0011	-0.0465	-0.0199	-0.0111	0.0546	-0.0029	0.0007	0.0353	0.0027	0.0899	26.6941	59.0813	123.3135
6	0.2593	0.0145	-0.1778	0.2337	-0.0233	0.4585	0.0067	-0.0224	-0.0026	0.0135	0.0079	-0.0287	0.0034	0.0564	-0.0146	0.0626	-0.0034	-0.0121	0.0596	-0.0083	0.0898	27.6457	23.8179	129.2667
7	0.5318	-0.1638	0.1481	0.2735	-0.1082	0.335	-0.0087	-0.0475	-0.058	0.0296	0.0199	0.0389	0.0322	-0.0592	-0.0112	0.0784	-0.0089	0.0093	0.0617	0.0061	0.0658	9.8021	17.4241	137.585
8	1.0936	0.1228	0.1638	1.0583	-0.0245	1.4158	0.0352	-0.0062	-0.0931	-0.0075	0.0021	-0.2324	0.2018	0.1693	-0.0372	0.0698	0.0242	-0.0084	0.0766	0.0093	0.1282	35.086	8.5781	136.8861
9	0.7192	-0.6517	-0.0579	1.1029	0.0073	0.4384	0.0092	0.0331	0.0767	-0.0008	0.02	0.0129	-0.0575	-0.0646	-0.0292	0.0711	-0.0091	-0.0033	0.0732	0.0069	0.0704	-3.9314	31.2425	120.0198
10	0.394	-0.102	0.1936	0.3188	-0.1579	0.463	0.0266	-0.0087	-0.0591	0.0011	-0.0097	-0.0366	0.0513	0.0275	-0.0169	0.0659	-0.0017	-0.0013	0.0397	-0.0063	0.0739	19.8825	8.6243	128.7769
11	0.1523	0.145	0.2328	0.35	0.2584	0.3725	-0.0003	0.0631	-0.0101	-0.0927	0.0197	-0.0292	-0.0125	0.0662	-0.0194	0.0797	-0.0023	0.0044	0.0887	0.0035	0.0176	10.7159	33.8745	75.9032
12	0.2759	-0.1075	0.0111	0.5935	0.0902	0.4678	0.0185	0.06	-0.0577	-0.0747	0.0038	0.0482	0.0703	-0.054	-0.0223	0.0752	-0.0048	-0.016	0.0924	-0.003	0.0258	0.6903	20.9215	83.0985
13	0.4462	-0.0467	0.0835	0.5459	-0.0929	0.8472	0.0017	0.054	0.099	-0.0932	0.0075	0.0285	-0.1561	-0.0749	-0.0092	0.1135	0.0002	-0.0218	0.0871	0.0074	0.0443	-1.6221	38.9569	69.9906
14	0.9268	0.2665	0.1973	2.0807	0.6582	0.992	0.0599	0.1184	-0.2487	-0.0097	0.0452	-0.3485	0.2064	0.2209	-0.1051	0.0729	0.0484	-0.0041	0.0691	-0.0257	0.1063	21.946	-3.5176	92.1383
15	0.1702	-0.0617	0.1652	0.3666	-0.0764	0.5689	-0.0039	0.0429	0.0276	-0.0417	-0.0016	0.0011	-0.0235	-0.0378	0.0055	0.0685	-0.0011	-0.0085	0.0918	-0.0061	0.0413	-2.4607	27.4411	84.9655
16	0.3658	0.0116	0.058	0.2682	-0.0322	0.4466	0.0157	0.1902	0.008	-0.0867	0.0214	-0.0911	-0.0518	0.1067	-0.0371	0.0403	-0.0094	0.0385	0.1352	-0.0214	0.0431	34.2869	28.4403	78.7275
17	0.6924	-0.0497	0.1921	0.6712	0.2485	0.5251	0.0082	0.292	-0.0753	-0.1701	0.033	-0.0426	-0.0626	0.13	-0.0412	0.074	-0.0091	0.0386	0.1997	-0.0281	0.0363	38.7054	33.8431	69.8604
18	0.6368	0.0999	-0.083	0.4808	0.1532	0.9704	-0.1001	0.0608	-0.0433	0.1017	0.0589	0.0003	-0.0115	0.0799	0.0412	0.1558	-0.0765	0.0207	0.259	0.0193	0.155	35.5024	46.3341	88.0517
19	1.4875	-1.047	0.3803	1.2479	-0.0115	0.3018	-0.0269	0.1669	0.018	-0.1013	-0.0159	0.0605	-0.1047	0.0475	0.0429	0.113	-0.026	0.0122	0.1064	0.0343	0.0425	25.7654	59.258	84.5998
20	0.3259	-0.1426	0.045	0.5166	0.1383	0.4758	0.0006	0.176	-0.0444	-0.0798	0.0417	-0.1301	0.0351	0.1714	-0.0423	0.0289	-0.0002	0.038	0.1568	-0.0506	0.0725	45.1108	33.0236	81.259

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	43 - 165
2	X-RAY DIFFRACTION	2	A	166 - 293
3	X-RAY DIFFRACTION	3	A	294 - 358
4	X-RAY DIFFRACTION	4	A	359 - 461
5	X-RAY DIFFRACTION	5	A	462 - 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 - 477
10	X-RAY DIFFRACTION	10	B	478 - 618
11	X-RAY DIFFRACTION	11	C	45 - 131
12	X-RAY DIFFRACTION	12	C	132 - 249
13	X-RAY DIFFRACTION	13	C	250 - 363
14	X-RAY DIFFRACTION	14	C	364 - 429
15	X-RAY DIFFRACTION	15	C	430 - 618
16	X-RAY DIFFRACTION	16	D	45 - 189
17	X-RAY DIFFRACTION	17	D	190 - 341
18	X-RAY DIFFRACTION	18	D	342 - 388
19	X-RAY DIFFRACTION	19	D	389 - 461
20	X-RAY DIFFRACTION	20	D	462 - 618

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