PDB-3vxi: Dye-decolorizing peroxidase (DyP) complex with ascorbic acid

ID or keywords:

Entry

Database: PDB / ID: 3vxi

Title

Dye-decolorizing peroxidase (DyP) complex with ascorbic acid

Components

DyP

Keywords

OXIDOREDUCTASE / DyP / Dye-decolorizing peroxidase /

ascorbic acid

Function / homology

Function and homology information

peroxidase activity /

heme binding /

metal ion binding
Similarity search - Function

Biological species

Bjerkandera adusta (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.5 Å

Authors

Sugano, Y. / Yoshida, T. / Tsuge, H.

Citation

Journal: to be published
Title: Dye-decolorizing peroxidase (DyP) complex with ascorbic acid
Authors: Sugano, Y. / Yoshida, T. / Tsuge, H.

History

Deposition	Sep 14, 2012	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Nov 7, 2012	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2	Jul 29, 2020	Group: Data collection / Derived calculations / Category: chem_comp / struct_site / struct_site_gen / Item: _chem_comp.type / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3	Nov 8, 2023	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3vxi.cif.gz	176.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3vxi.ent.gz	139.1 KB	Display	PDB format
PDBx/mmJSON format	3vxi.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vx/3vxi ftp://data.pdbj.org/pub/pdb/validation_reports/vx/3vxi	HTTPS FTP

-
Related structure data

Related structure data	3afvS 3vxj S: Starting model for refinement
Similar structure data	2d3q-1 3vxj-d 5udy-d 3siy-2 3mm2-d 4w7j-4 3s52-1 3afv-d 3qsm-1 4bjz-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

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: DyP

hetero molecules

48.3 kDa, 1 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)	46.892, 95.912, 50.333
Angle α, β, γ (deg.)	90.000, 103.810, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	DyP / dye-decolorizing peroxidase Mass: 47497.344 Da / Num. of mol.: 1 / Fragment: UNP residues 57-498 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bjerkandera adusta (fungus) / Strain: Dec 1 / Gene: dyp / Plasmid: pTAex3 / Production host: Aspergillus oryzae (mold) / Strain (production host): M-2-3 / References: UniProt: Q8WZK8, dye decolorizing peroxidase
#2: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄
#3: Sugar	ChemComp-ASC / ASCORBIC ACID / Vitamin C / Vitamin C Type: L-saccharide / Mass: 176.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₈O₆ / Comment: medication*YM
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.31 Å³/Da / Density % sol: 46.85 % / Mosaicity: 0.456 °
Crystal grow	Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG8000, pH 6.0, vapor diffusion, hanging drop, temperature 278K

-
Data collection

Diffraction

Mean temperature: 95 K

Diffraction source

Source:

SYNCHROTRON / Site:

Photon Factory

/ Beamline: AR-NW12A / Wavelength: 1 Å

Detector

Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 10, 2012

Radiation

Monochromator: Numerical link type Si(111) double crystal monochromator, liquid nitrogen cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Redundancy: 3.8 % / Av σ(I) over netI: 29.12 / Number: 259431 / R_merge(I) obs: 0.05 / Χ²: 1.28 / D res high: 1.5 Å / D res low: 50 Å / Num. obs: 68745 / % possible obs: 99.5

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
4.07	50	98.8	1	0.025	1.063	3.7
3.23	4.07	99.6	1	0.025	1.058	3.8
2.82	3.23	99.9	1	0.031	1.139	3.8
2.56	2.82	99.9	1	0.037	1.173	3.8
2.38	2.56	100	1	0.042	1.239	3.8
2.24	2.38	100	1	0.046	1.254	3.8
2.13	2.24	99.9	1	0.052	1.282	3.8
2.04	2.13	99.9	1	0.059	1.312	3.8
1.96	2.04	99.9	1	0.067	1.302	3.8
1.89	1.96	99.7	1	0.08	1.325	3.8
1.83	1.89	99.6	1	0.096	1.389	3.8
1.78	1.83	99.7	1	0.113	1.338	3.8
1.73	1.78	99.3	1	0.13	1.338	3.8
1.69	1.73	99.5	1	0.155	1.366	3.8
1.65	1.69	99.3	1	0.175	1.355	3.8
1.62	1.65	99.1	1	0.194	1.322	3.8
1.58	1.62	99.2	1	0.212	1.35	3.8
1.55	1.58	99	1	0.235	1.309	3.7
1.53	1.55	98.9	1	0.259	1.305	3.7
1.5	1.53	98.9	1	0.283	1.331	3.7

Reflection

Resolution: 1.5→50 Å / Num. obs: 68745 / % possible obs: 99.5 % / Redundancy: 3.8 % / R_merge(I) obs: 0.05 / Χ²: 1.277 / Net I/σ(I): 12.7

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
1.5-1.53	3.7	0.283	3422	1.331	1	98.9
1.53-1.55	3.7	0.259	3368	1.305	1	98.9
1.55-1.58	3.7	0.235	3397	1.309	1	99
1.58-1.62	3.8	0.212	3464	1.35	1	99.2
1.62-1.65	3.8	0.194	3344	1.322	1	99.1
1.65-1.69	3.8	0.175	3465	1.355	1	99.3
1.69-1.73	3.8	0.155	3433	1.366	1	99.5
1.73-1.78	3.8	0.13	3414	1.338	1	99.3
1.78-1.83	3.8	0.113	3425	1.338	1	99.7
1.83-1.89	3.8	0.096	3422	1.389	1	99.6
1.89-1.96	3.8	0.08	3456	1.325	1	99.7
1.96-2.04	3.8	0.067	3427	1.302	1	99.9
2.04-2.13	3.8	0.059	3483	1.312	1	99.9
2.13-2.24	3.8	0.052	3430	1.282	1	99.9
2.24-2.38	3.8	0.046	3448	1.254	1	100
2.38-2.56	3.8	0.042	3461	1.239	1	100
2.56-2.82	3.8	0.037	3456	1.173	1	99.9
2.82-3.23	3.8	0.031	3466	1.139	1	99.9
3.23-4.07	3.8	0.025	3466	1.058	1	99.6
4.07-50	3.7	0.025	3498	1.063	1	98.8

-
Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	4 Å	33.02 Å
Translation	4 Å	33.02 Å

-
Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
MOLREP		phasing
REFMAC		refinement
PDB_EXTRACT	3.11	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3AFV

3afv

Resolution: 1.5→48.88 Å / Cor.coef. F_o:F_c: 0.958 / Cor.coef. F_o:F_c free: 0.952 / WR_factor R_free: 0.1863 / WR_factor R_work: 0.1678 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8975 / SU B: 2.029 / SU ML: 0.038 / SU R Cruickshank DPI: 0.0693 / SU R_free: 0.0684 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1926	3483	5.1 %	RANDOM
R_work	0.1727	-	-	-
obs	0.1738	68666	99.34 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso max: 24.82 Å² / B_iso mean: 11.251 Å² / B_iso min: 2 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.38 Å²	0 Å²	0.33 Å²
2-	-	-0.87 Å²	0 Å²
3-	-	-	-0.35 Å²

Refinement step

Cycle: LAST / Resolution: 1.5→48.88 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3331	0	55	131	3517

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	3480
X-RAY DIFFRACTION	r_angle_refined_deg	1.235	1.988	4763
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.779	5	437
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.455	24.908	163
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.802	15	494
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.252	15	16
X-RAY DIFFRACTION	r_chiral_restr	0.082	0.2	512
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	2768

LS refinement shell

Resolution: 1.499→1.538 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.214	251	-
R_work	0.198	4705	-
all	-	4956	-
obs	-	-	97.62 %

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	1.1831	-0.0039	-0.3719	2.4059	-1.3954	3.1547	0.0264	-0.1135	0.0322	0.2859	0.0074	-0.0812	-0.1818	0.0014	-0.0338	0.0469	-0.0114	-0.0165	0.0509	-0.0018	0.039	13.7257	-6.9413	27.363
2	0.9208	0.4111	0.2423	2.218	-0.2432	0.673	0.0452	0.0115	-0.0541	0.0303	-0.0329	-0.1479	0.0109	0.0846	-0.0123	0.019	0.0079	0.0112	0.051	0.0018	0.0527	18.3065	-15.5147	13.0838
3	1.6838	-0.1163	-0.8593	0.2936	-0.8157	1.2268	0.152	-0.2225	0.1405	0.1552	-0.1106	-0.1179	-0.2203	0.2897	-0.0413	0.0461	-0.0445	-0.0268	0.0573	-0.0048	0.0791	21.4476	-5.7155	22.1801
4	3.0752	-2.4401	0.3851	4.8897	-1.6658	2.7751	-0.0229	-0.0413	-0.269	0.0274	0.0134	0.2002	0.1684	-0.0173	0.0095	0.0439	-0.0016	0.005	0.0285	-0.0042	0.0528	4.734	-22.4794	13.0041
5	0.0041	0.1972	-0.4565	0.7464	-0.3884	1.2857	-0.0293	0.0109	-0.0335	0.0322	0.0013	0.0729	0.0446	-0.0533	0.028	0.0425	-0.0118	0.0061	0.0316	0.003	0.0547	-0.2198	-19.3703	16.9357
6	0.4882	-0.0287	-0.0259	0.7702	-0.0343	0.3086	0.0247	0.0331	-0.0009	-0.1265	-0.0463	0.0182	-0.0161	-0.0329	0.0216	0.0507	0.0024	-0.004	0.0359	-0.009	0.0222	3.2004	-9.8263	5.3507
7	2.6238	2.9929	0.4732	8.4284	0.4904	-0.3919	-0.1627	0.1415	-0.0545	-0.3771	0.1688	-0.3445	-0.0017	0.0543	-0.0061	0.0147	-0.0164	0.0132	0.0605	-0.0049	0.0287	24.6704	-11.6315	8.5748
8	0.4746	1.7841	0.475	14.6806	2.2757	0.274	-0.0226	0.0421	0.0036	-0.4385	0.0281	-0.1942	0	0.046	-0.0054	0.0914	0.0217	0.0226	0.0343	0.0087	0.0192	14.699	-8.0696	3.8468
9	1.9073	-1.3589	-0.3827	1.436	0.4529	2.5256	0.0082	-0.1055	0.2265	-0.0536	0.0077	-0.2967	-0.0634	0.1392	-0.0159	0.0305	-0.0115	0.0075	0.0373	0.0068	0.0756	10.9843	12.3158	9.2189
10	0.2039	-0.4558	0.1772	6.089	-2.3788	0.6612	-0.0708	0.0067	0.0535	0.4213	-0.0789	-0.4183	-0.1052	0.0747	0.1497	0.0898	0.004	-0.0409	0.0351	-0.0004	0.0216	6.8627	3.9528	30.5818
11	0.6634	0.0422	0.0528	1.3209	-0.3797	0.4985	-0.0118	-0.0407	-0.0244	0.1768	-0.0026	0.0264	-0.006	0.0232	0.0144	0.057	-0.0072	0.0027	0.0347	0.003	0.023	2.7568	-13.0301	27.2845
12	0.393	0.5064	-0.6867	3.8073	-1.9727	1.4694	0.0107	0.0728	0.0194	-0.2562	-0.0303	0.0133	0.0694	-0.0365	0.0196	0.0519	0.0056	0.003	0.0515	0.0052	0.0366	3.9255	2.111	3.1957
13	0.4167	-0.8702	-0.8004	2.1627	1.485	2.2704	0.0195	0.0083	0.0019	-0.0639	-0.0011	-0.0126	-0.0687	0.0673	-0.0185	0.0471	-0.0004	0.0019	0.0391	0.0058	0.0365	-3.8313	22.919	4.0354
14	0.2161	0.9152	-0.996	4.624	-4.5455	3.5486	0.0064	-0.0115	0.0003	-0.0604	-0.1915	-0.2408	0.0283	0.1756	0.185	0.0581	-0.0026	0.0094	0.0518	0.0116	0.0511	-0.6524	25.5066	5.9628
15	0.4988	-0.1617	-0.0245	0.9405	-0.086	0.3745	-0.0088	-0.0179	0.0289	0.0904	-0.0047	-0.0376	-0.0422	0.0302	0.0135	0.0482	-0.0022	0.002	0.0369	-0.0033	0.0311	-2.0487	16.9047	20.2503
16	0.7855	0.0394	-0.6061	0.8019	-0.2877	1.1823	0.0235	0.0142	0.0344	0.0621	-0.0018	-0.0079	-0.0629	-0.0081	-0.0218	0.0436	-0.0034	-0.0034	0.0386	-0.0046	0.0391	2.9938	3.2336	17.3204
17	19.8402	-7.9735	7.3881	13.5419	0.432	8.7544	-0.0289	1.1119	1.477	-0.7061	-0.9171	-0.8266	-0.6499	0.8427	0.946	0.1168	0.0249	0.0096	0.0858	0.1611	0.043	8.1384	13.3846	-6.921
18	0.071	-0.1028	0.0687	0.6706	-0.1202	0.3127	0.0017	-0.0054	-0.0079	0.007	-0.0038	0.0674	0.0137	-0.0051	0.0021	0.0362	-0.0026	0.0021	0.0412	-0.0014	0.0353	-3.6795	-0.7725	14.8835
19	0.6027	-0.6263	-0.2237	1.1741	0.3612	0.6525	0.0298	0.0345	-0.0787	-0.068	-0.065	0.1489	-0.007	-0.0775	0.0352	0.0255	-0.0019	-0.0034	0.04	-0.0043	0.0512	-11.8682	12.5225	8.7873
20	0.8944	-0.3614	0.6382	1.2203	-0.8145	1.6155	0.0447	-0.0289	-0.0647	-0.0347	-0.0454	-0.0632	0.1072	0.0652	0.0007	0.0457	-0.0026	0.0027	0.0446	-0.0055	0.0451	8.4353	-14.7492	16.5439

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	5 - 19
2	X-RAY DIFFRACTION	2	A	20 - 48
3	X-RAY DIFFRACTION	3	A	49 - 71
4	X-RAY DIFFRACTION	4	A	72 - 78
5	X-RAY DIFFRACTION	5	A	79 - 94
6	X-RAY DIFFRACTION	6	A	95 - 126
7	X-RAY DIFFRACTION	7	A	127 - 146
8	X-RAY DIFFRACTION	8	A	147 - 156
9	X-RAY DIFFRACTION	9	A	157 - 171
10	X-RAY DIFFRACTION	10	A	172 - 194
11	X-RAY DIFFRACTION	11	A	195 - 219
12	X-RAY DIFFRACTION	12	A	220 - 228
13	X-RAY DIFFRACTION	13	A	229 - 246
14	X-RAY DIFFRACTION	14	A	247 - 257
15	X-RAY DIFFRACTION	15	A	258 - 317
16	X-RAY DIFFRACTION	16	A	318 - 338
17	X-RAY DIFFRACTION	17	A	339 - 350
18	X-RAY DIFFRACTION	18	A	351 - 381
19	X-RAY DIFFRACTION	19	A	382 - 420
20	X-RAY DIFFRACTION	20	A	421 - 442

-
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://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

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
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

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Phasing

-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

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
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