PDB-4mor: Pyranose 2-oxidase H450G/V546C double mutant with 3-fluorinated g...

ID or keywords:

Entry

Database: PDB / ID: 4mor

Title

Pyranose 2-oxidase H450G/V546C double 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: 1.5 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_label_asym_id / _struct_ref_seq_dif.details Description: Carbohydrate remediation / Provider: repository / Type: Remediation

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4mor.cif.gz	949.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4mor.ent.gz	789.5 KB	Display	PDB format
PDBx/mmJSON format	4mor.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4mor_validation.pdf.gz	1.9 MB	Display	wwPDB validaton report
Full document	4mor_full_validation.pdf.gz	1.9 MB	Display
Data in XML	4mor_validation.xml.gz	115.3 KB	Display
Data in CIF	4mor_validation.cif.gz	177.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mo/4mor ftp://data.pdbj.org/pub/pdb/validation_reports/mo/4mor	HTTPS FTP

-
Related structure data

Related structure data	4moeC 4mofC 4mogC 4mohC 4moiC 4mojC 4mokC 4molC 4momC 4mooC 4mopC 4moqC 4mosC 1tt0 2igo 3pl8 C: citing same article (ref.)
Similar structure data	3k4c-d 2igk-1 4mol-d 4mop-d 3lsk-d 4mof-1 3fdy-1 3k4l-1 2f6c-1 2ign-2 2igk-2 4moo-1 4mok-d 1tt0-d 3lsm-1 1tzl-2 3pl8-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
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)	100.242, 102.469, 137.840
Angle α, β, γ (deg.)	90.00, 91.09, 90.00
Int Tables number	4
Space group name H-M	P12₁1

-
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-2H5 / 3-deoxy-3-fluoro-beta-D-galactopyranose

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

-
Non-polymers , 4 types, 3072 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.: 2 / Source method: obtained synthetically / Formula: C₆H₁₃NO₄S / Comment: pH buffer*YM
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 3062 / 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: 2.51 Å³/Da / Density % sol: 51.01 %
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

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.946495 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 12, 2013 / Details: unfocused
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.946495 Å / Relative weight: 1
Reflection	Resolution: 1.5→49.33 Å / Num. all: 442699 / Num. obs: 442699 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Net I/σ(I): 11.9
Reflection shell	Resolution: 1.5→1.6 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 1.6 / % possible all: 99.7

-
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: 1.5→49.33 Å / Cor.coef. F_o:F_c: 0.975 / Cor.coef. F_o:F_c free: 0.959 / SU B: 2.605 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.198	1107	0.3 %	RANDOM
R_work	0.156	-	-	-
obs	0.156	441592	99.7 %	-
all	-	441592	-	-

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: 25.89 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.06 Å²	0 Å²	-0.05 Å²
2-	-	0.09 Å²	0 Å²
3-	-	-	0.96 Å²

Refinement step

Cycle: LAST / Resolution: 1.5→49.33 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18116	0	340	3062	21518

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.027	0.02	19109
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	12920
X-RAY DIFFRACTION	r_angle_refined_deg	2.283	1.968	26021
X-RAY DIFFRACTION	r_angle_other_deg	1.175	3	31507
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.03	5	2356
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.766	24.547	906
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.571	15	3078
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.915	15	109
X-RAY DIFFRACTION	r_chiral_restr	0.201	0.2	2841
X-RAY DIFFRACTION	r_gen_planes_refined	0.013	0.021	21159
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3846
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: 1.5→1.58 Å / Total num. of bins used: 10

	R_factor	Num. reflection	% reflection
R_free	0.303	161	-
R_work	0.297	63323	-
obs	-	-	99.67 %

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	0.2526	0.0802	0.1694	0.2516	0.078	0.3334	0.0008	-0.019	0.0137	0.0132	-0.0017	-0.025	0.0257	-0.0146	0.0008	0.0803	0.004	0.0059	0.0972	-0.0018	0.0974	19.0971	9.2129	59.9383
2	0.4954	-0.1315	-0.1464	0.2824	0.1122	0.3214	-0.0236	-0.0149	0.0399	0.0235	0.0192	-0.0504	-0.0006	0.0348	0.0043	0.0739	-0.0024	-0.0191	0.0817	-0.0114	0.1094	37.5517	16.9818	65.1744
3	0.9655	0.0896	-0.2956	0.8685	0.4184	1.2277	0.0054	0.0302	0.1069	-0.0195	-0.0115	0.143	-0.1431	-0.2077	0.0061	0.0697	0.024	-0.0123	0.1021	-0.0172	0.1451	11.667	25.0865	65.3417
4	1.0852	-0.9189	0.1475	1.2566	0.0635	0.3159	-0.018	-0.0294	-0.079	0.0728	0.0793	-0.1012	0.075	0.0903	-0.0613	0.0644	0.0054	-0.0079	0.0915	-0.0124	0.1151	52.9463	-0.8526	49.954
5	0.3849	-0.0864	-0.1295	0.3147	0.2065	0.4132	0.0004	0.014	0.0534	-0.0052	0.0018	-0.0031	-0.0301	-0.015	-0.0022	0.0701	-0.0027	-0.0044	0.0677	0.0072	0.0956	28.002	20.6238	54.4563
6	0.2272	0.0599	-0.0439	0.2915	-0.1627	0.3421	0.0086	0.1006	0.0104	-0.0995	-0.0043	-0.0616	0.0044	0.0035	-0.0043	0.0898	0.0149	0.0376	0.1178	-0.0228	0.0553	31.9949	-11.6597	11.5964
7	0.2697	-0.1213	-0.1116	0.7228	0.1801	0.5766	0.0352	0.1243	0.0097	-0.168	-0.0507	-0.1028	-0.0386	0.0758	0.0155	0.1007	0.0119	0.0758	0.1618	0.0266	0.0654	41.2703	3.8202	2.0685
8	1.5545	0.0062	0.0495	1.8872	0.0468	1.5917	0.1117	0.1032	-0.2848	-0.1711	-0.077	-0.2474	0.3649	0.2015	-0.0347	0.1595	0.0677	0.0522	0.1173	-0.0318	0.1523	46.4579	-21.2832	5.407
9	1.0354	-0.5824	0.1069	0.9703	-0.0258	0.4448	-0.0421	0.1288	0.0931	-0.0593	0.0084	0.0627	-0.1274	-0.0191	0.0337	0.1233	-0.0197	0.0149	0.1182	0.0372	0.0733	26.7451	21.6181	18.5465
10	0.3844	-0.1491	-0.0865	0.6014	0.1867	0.5898	0.0072	0.1143	-0.0528	-0.1012	-0.0132	-0.1438	0.0491	0.1165	0.006	0.0574	0.0129	0.0622	0.1371	0.0011	0.0927	47.644	-5.1944	12.607
11	0.2066	0.111	0.1685	0.3452	0.2937	0.4364	-0.0062	0.0567	0.0025	-0.0929	0.007	-0.0239	-0.0398	0.0328	-0.0008	0.1078	0.0065	0.0095	0.1101	0.015	0.05	10.7754	-0.2465	10.7898
12	0.2684	0.0041	0.0606	0.5996	-0.3611	0.9361	0.0269	0.0391	-0.0192	-0.0902	-0.016	0.0382	0.0946	-0.0709	-0.011	0.1104	-0.0012	-0.0144	0.1153	-0.0239	0.0479	2.0845	-19.9948	6.4307
13	0.4154	-0.2179	0.1649	0.6979	-0.2493	0.7941	-0.0221	0.0586	0.0797	-0.0815	0.0146	0.0245	-0.1459	-0.1246	0.0075	0.1338	-0.0015	-0.0135	0.1659	-0.015	0.0877	-0.4611	-1.4406	9.9534
14	26.3677	14.5649	-6.7155	29.5321	3.8223	14.219	1.7082	-0.8516	-2.7485	1.9155	-0.8487	-3.3813	1.298	0.2216	-0.8595	0.3678	-0.0316	-0.367	0.0624	0.1378	0.5634	35.405	-46.3124	27.582
15	0.1973	-0.0335	0.0734	0.3865	-0.0632	0.4402	0.0024	0.0492	-0.003	-0.0416	-0.0083	-0.0247	0.019	-0.0426	0.006	0.0867	-0.0093	-0.0059	0.1232	-0.0114	0.0524	2.9295	-15.2185	17.3966
16	0.2628	0.0404	-0.1451	0.2575	-0.0412	0.3974	0.0019	-0.0152	-0.0036	0.0082	-0.0069	-0.032	-0.0077	0.0348	0.0051	0.0716	-0.0008	-0.0094	0.0854	-0.0031	0.0922	28.5524	-13.2007	61.0474
17	0.6979	-0.1934	0.1904	0.3505	-0.1091	0.3352	0.0017	-0.0306	-0.0548	0.0132	0.006	0.0332	0.0497	-0.0531	-0.0077	0.0969	-0.01	0.0165	0.0991	0.0033	0.0875	10.2732	-19.9025	69.2457
18	1.4343	0.0936	0.2327	0.8257	-0.4823	1.2611	0.0267	0.0278	-0.106	-0.0001	-0.0047	-0.1842	0.1769	0.1569	-0.022	0.0932	0.0223	-0.0027	0.1097	0.0097	0.1381	36.6618	-28.0585	69.1392
19	0.7699	-0.4745	-0.0482	0.6765	-0.0528	0.2904	0.0193	0.0194	0.0761	-0.0031	0.0021	0.0113	-0.0432	-0.0584	-0.0214	0.0827	-0.0089	-0.0025	0.1006	0.0011	0.0753	-1.6306	-7.3713	51.5335
20	0.3799	-0.0961	0.1662	0.3376	-0.2101	0.4582	0.0179	-0.0129	-0.0603	0.0072	-0.0046	-0.0295	0.0382	0.0218	-0.0133	0.0847	-0.0051	0.0005	0.0756	-0.0043	0.0833	20.7452	-28.198	60.6326

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	43 - 166
2	X-RAY DIFFRACTION	2	A	168 - 293
3	X-RAY DIFFRACTION	3	A	294 - 356
4	X-RAY DIFFRACTION	4	A	357 - 451
5	X-RAY DIFFRACTION	5	A	452 - 618
6	X-RAY DIFFRACTION	6	B	46 - 163
7	X-RAY DIFFRACTION	7	B	164 - 298
8	X-RAY DIFFRACTION	8	B	299 - 356
9	X-RAY DIFFRACTION	9	B	357 - 469
10	X-RAY DIFFRACTION	10	B	470 - 618
11	X-RAY DIFFRACTION	11	C	46 - 166
12	X-RAY DIFFRACTION	12	C	168 - 285
13	X-RAY DIFFRACTION	13	C	286 - 382
14	X-RAY DIFFRACTION	14	C	383 - 391
15	X-RAY DIFFRACTION	15	C	392 - 618
16	X-RAY DIFFRACTION	16	D	43 - 166
17	X-RAY DIFFRACTION	17	D	168 - 293
18	X-RAY DIFFRACTION	18	D	294 - 354
19	X-RAY DIFFRACTION	19	D	355 - 481
20	X-RAY DIFFRACTION	20	D	482 - 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://pdbjlvh1.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

-
Protein / Sugars , 2 types, 8 molecules ABCD

-
Non-polymers , 4 types, 3072 molecules

-
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

-Protein / Sugars , 2 types, 8 molecules ABCD

-Non-polymers , 4 types, 3072 molecules

-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

-
Protein / Sugars , 2 types, 8 molecules ABCD

-
Non-polymers , 4 types, 3072 molecules

-
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