PDB-4mom: Pyranose 2-oxidase H450G mutant with 3-fluorinated galactose

ID or keywords:

Entry

Database: PDB / ID: 4mom

Title

Pyranose 2-oxidase H450G mutant with 3-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: 1.9 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	Mar 7, 2018	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
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_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3	Nov 27, 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	4mom.cif.gz	903.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4mom.ent.gz	754.4 KB	Display	PDB format
PDBx/mmJSON format	4mom.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4mom_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	4mom_full_validation.pdf.gz	1.5 MB	Display
Data in XML	4mom_validation.xml.gz	110.9 KB	Display
Data in CIF	4mom_validation.cif.gz	145.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mo/4mom ftp://data.pdbj.org/pub/pdb/validation_reports/mo/4mom	HTTPS FTP

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Related structure data

Related structure data	4moeC 4mofC 4mogC 4mohC 4moiC 4mojC 4mokC 4molC 4mooC 4mopC 4moqC 4morC 4mosC 1tt0 2igo 3pl8 C: citing same article (ref.)
Similar structure data	3lsh-d 3lsi-1 4moe-d 3k4m-1 1tzl-2 3k4n-1 2igo-1 2ign-1 1tzl-1 3k4k-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

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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

287 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)	99.896, 102.423, 137.365
Angle α, β, γ (deg.)	90.00, 91.19, 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-2H5 / 3-deoxy-3-fluoro-beta-D-galactopyranose / 3-deoxy-3-fluoro-beta-D-galactose / 3-deoxy-3-fluoro-D-galactose / 3-deoxy-3-fluoro-galactose

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, 1077 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.: 2 / Source method: obtained synthetically / Formula: C₆H₁₃NO₄S / Comment: pH buffer*YM
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1067 / 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: 2.49 Å³/Da / Density % sol: 50.65 %
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: I911-3 / Wavelength: 1 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 5, 2009 / Details: Rh-coated Si mirrors
Radiation	Monochromator: Double-crystal monochromator, Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.9→57.14 Å / Num. all: 215840 / Num. obs: 215840 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Net I/σ(I): 10.3
Reflection shell	Resolution: 1.9→2 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.6 / % possible all: 99.1

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.9→50 Å / Cor.coef. F_o:F_c: 0.923 / Cor.coef. F_o:F_c free: 0.896 / SU B: 9.92 / SU ML: 0.149 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.28	3865	1.8 %	RANDOM
R_work	0.238	-	-	-
obs	0.239	211975	99.2 %	-
all	-	211975	-	-

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: 24.79 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.72 Å²	0 Å²	-1.24 Å²
2-	-	0.07 Å²	0 Å²
3-	-	-	1.59 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18112	0	343	1067	19522

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.02	18934
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	12776
X-RAY DIFFRACTION	r_angle_refined_deg	1.96	1.966	25739
X-RAY DIFFRACTION	r_angle_other_deg	1.013	3	31079
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.122	5	2296
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.902	24.497	894
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.835	15	3024
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.744	15	108
X-RAY DIFFRACTION	r_chiral_restr	0.134	0.2	2808
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.021	20896
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3804
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: 1.9→2 Å / Total num. of bins used: 10

	R_factor	Num. reflection	% reflection
R_free	0.379	548	-
R_work	0.33	30198	-
obs	-	-	99.07 %

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	0.2945	0.0588	0.2577	0.3626	0.0426	0.358	0.0243	0.007	-0.0144	0.016	-0.0094	-0.0245	0.0361	-0.0058	-0.0149	0.074	-0.0088	-0.0052	0.09	-0.0061	0.0777	17.152	46.1545	128.045
2	0.7666	-0.1132	-0.2461	0.2831	0.0889	0.3536	-0.0253	-0.0307	0.0524	0.03	0.0242	-0.0983	0.0097	0.0503	0.0011	0.0657	-0.009	-0.0322	0.08	-0.0058	0.0857	35.4957	53.8053	133.7153
3	1.352	0.0666	-0.5012	0.8454	0.2746	1.2967	0.0129	0.0372	0.0657	-0.0229	-0.0443	0.1584	-0.1611	-0.2332	0.0315	0.0674	0.0114	-0.0324	0.0863	-0.03	0.1372	10.2846	62.179	133.6738
4	1.5388	-0.7278	0.2831	1.2672	0.1186	0.5242	-0.0114	-0.0209	-0.1552	0.0422	0.0594	-0.0786	0.0807	0.0841	-0.0481	0.0494	0.0031	-0.0141	0.0809	-0.0091	0.1156	48.5995	36.3307	117.6934
5	0.3439	-0.085	-0.1788	0.2762	0.1368	0.4083	0.01	0.0387	0.0514	-0.0144	-0.0054	0.0129	-0.0597	-0.0203	-0.0046	0.0476	0.0024	-0.0214	0.0588	-0.0069	0.0822	24.8728	60.9557	124.2166
6	0.3123	0.0171	-0.196	0.2177	-0.0231	0.3783	-0.0028	0.0151	0.0297	0.0149	0.0014	-0.0366	-0.0079	0.0409	0.0014	0.0599	-0.0064	-0.0248	0.0869	-0.0004	0.0846	26.9468	23.7567	129.3512
7	1.0564	-0.1879	0.312	0.2183	-0.1226	0.3929	-0.0041	-0.0032	-0.1221	0.0265	0.0154	0.058	0.0181	-0.0267	-0.0112	0.086	-0.0113	-0.009	0.0686	0.0048	0.0705	9.4519	17.5715	137.6458
8	1.8139	-0.114	0.0191	1.1587	-0.2161	1.4731	0.0358	0.0441	-0.0555	-0.0374	-0.0521	-0.1362	0.173	0.2389	0.0162	0.0743	0.025	-0.0199	0.0949	0.0236	0.1052	34.3511	8.4687	137.0261
9	1.0517	-0.6787	0.0551	1.0727	-0.1793	0.6414	0.021	0.0173	0.0852	-0.0115	0.0022	0.0076	-0.0598	-0.0506	-0.0232	0.0624	-0.0129	-0.0168	0.0844	-0.0018	0.0671	-4.6961	31.3564	120.0157
10	0.4632	-0.1438	0.2576	0.3119	-0.1508	0.5927	0.008	0.0243	-0.0323	-0.006	0.0011	-0.0295	0.0595	0.0446	-0.0092	0.0705	-0.0094	-0.0218	0.0654	0.0048	0.0694	19.1527	8.5318	128.8103
11	0.3294	0.0733	0.217	0.2416	0.1546	0.2666	0.0015	0.0175	0.015	-0.0797	0.0042	-0.0568	-0.0166	0.0548	-0.0057	0.1042	0.0011	-0.0103	0.0825	0.0168	0.0361	9.3609	36.9881	80.1073
12	0.2002	-0.024	0.1008	0.7167	-0.3629	0.6515	0.0479	0.0348	-0.0223	-0.091	-0.0431	0.0606	0.0709	-0.0215	-0.0048	0.1262	-0.0031	-0.0283	0.0977	-0.0128	0.0127	0.261	19.6613	74.4483
13	1.4057	-0.2314	-0.2501	1.1959	-0.2564	2.3082	0.0155	0.0173	0.1978	-0.0938	0.0335	-0.0137	-0.3025	-0.2395	-0.049	0.1458	0.0191	-0.0344	0.0729	0.0161	0.0439	-5.9363	44.5659	73.5886
14	1.0088	-0.3619	0.0876	1.5658	-0.0268	0.7639	-0.006	0.116	-0.0217	-0.0596	0.0072	-0.2146	0.1488	0.1162	-0.0011	0.1243	-0.004	-0.0114	0.1146	-0.0245	0.0448	15.9758	4.6624	92.1728
15	0.2281	-0.1582	0.236	0.3412	-0.1545	0.6717	-0.0033	0.0045	0.0203	-0.0779	0.0224	0.0203	-0.0421	-0.1226	-0.0192	0.0836	0.0087	-0.0378	0.0985	0.0048	0.0281	-6.2864	30.8668	83.2531
16	0.3657	0.0608	-0.1176	0.2922	-0.0661	0.2838	0.0145	0.1185	-0.0056	-0.1151	0.0169	-0.0585	-0.0115	0.0189	-0.0314	0.0614	0.0009	0.0208	0.0953	-0.0231	0.0285	30.5164	25.3364	80.0352
17	0.4255	-0.0268	-0.0791	1.0321	0.4174	0.5794	-0.0021	0.1828	-0.0012	-0.1783	-0.0169	-0.1005	-0.0634	0.071	0.019	0.1038	-0.0005	0.0381	0.1426	0.016	0.0236	39.2567	41.1297	70.6921
18	2.1038	-0.2755	-0.0101	1.2984	0.6495	2.1129	-0.0716	0.1563	-0.3769	-0.0974	0.1226	-0.2681	0.2414	0.1826	-0.051	0.0663	0.0159	0.0572	0.0754	-0.0596	0.1544	44.9067	16.2734	73.6449
19	1.4037	-0.7988	0.1527	1.2639	-0.103	0.6889	-0.0536	0.0827	0.0686	-0.0759	0.0392	0.0285	-0.1119	-0.0292	0.0144	0.1119	-0.02	-0.001	0.1008	0.0245	0.0527	25.4865	58.4412	87.2284
20	0.2786	-0.1894	-0.2251	0.6005	0.2277	0.5462	-0.0064	0.085	-0.0628	-0.1218	0.0141	-0.1372	0.0381	0.1056	-0.0077	0.0424	0.0014	0.0418	0.1192	-0.0522	0.0946	46.5359	31.3118	80.4759

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	43 - 160
2	X-RAY DIFFRACTION	2	A	161 - 293
3	X-RAY DIFFRACTION	3	A	294 - 357
4	X-RAY DIFFRACTION	4	A	358 - 472
5	X-RAY DIFFRACTION	5	A	473 - 618
6	X-RAY DIFFRACTION	6	B	43 - 157
7	X-RAY DIFFRACTION	7	B	158 - 293
8	X-RAY DIFFRACTION	8	B	294 - 356
9	X-RAY DIFFRACTION	9	B	357 - 476
10	X-RAY DIFFRACTION	10	B	477 - 618
11	X-RAY DIFFRACTION	11	C	45 - 157
12	X-RAY DIFFRACTION	12	C	158 - 293
13	X-RAY DIFFRACTION	13	C	294 - 359
14	X-RAY DIFFRACTION	14	C	360 - 471
15	X-RAY DIFFRACTION	15	C	472 - 618
16	X-RAY DIFFRACTION	16	D	45 - 158
17	X-RAY DIFFRACTION	17	D	159 - 295
18	X-RAY DIFFRACTION	18	D	296 - 358
19	X-RAY DIFFRACTION	19	D	359 - 474
20	X-RAY DIFFRACTION	20	D	475 - 618

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Yorodumi