PDB-8r2u: Crystal structure of hydroquinone-2-hydroxylase from Trametes ver...

ID or keywords:

Entry

Database: PDB / ID: 8r2u

Title

Crystal structure of hydroquinone-2-hydroxylase from Trametes versicolor (TvMNX3)

Components

Phenol 2-monooxygenase

Keywords

OXIDOREDUCTASE / fungi / hydroquinone / hydroxylase

Function / homology

FLAVIN-ADENINE DINUCLEOTIDE

Function and homology information

Biological species

Trametes versicolor (turkey-tail fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.41 Å

Authors

Zahn, M. / Kuatsjah, E. / Salvachua, D.

Funding support

United Kingdom, 1items

Citation

Journal: Cell Rep / Year: 2024
Title: Biochemical and structural characterization of enzymes in the 4-hydroxybenzoate catabolic pathway of lignin-degrading white-rot fungi.
Authors: Kuatsjah, E. / Schwartz, A. / Zahn, M. / Tornesakis, K. / Kellermyer, Z.A. / Ingraham, M.A. / Woodworth, S.P. / Ramirez, K.J. / Cox, P.A. / Pickford, A.R. / Salvachua, D.

History

Deposition	Nov 7, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 13, 2024	Provider: repository / Type: Initial release
Revision 1.1	Dec 4, 2024	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8r2u.cif.gz	1.2 MB	Display	PDBx/mmCIF format
PDB format	pdb8r2u.ent.gz	769.7 KB	Display	PDB format
PDBx/mmJSON format	8r2u.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8r2u_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	8r2u_full_validation.pdf.gz	1.5 MB	Display
Data in XML	8r2u_validation.xml.gz	98 KB	Display
Data in CIF	8r2u_validation.cif.gz	127.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r2/8r2u ftp://data.pdbj.org/pub/pdb/validation_reports/r2/8r2u	HTTPS FTP

-
Related structure data

Related structure data	8r2tC 8r2vC 8r2wC 8r2xC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Phenol 2-monooxygenase

B: Phenol 2-monooxygenase

C: Phenol 2-monooxygenase

D: Phenol 2-monooxygenase

hetero molecules

279 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Phenol 2-monooxygenase

C: Phenol 2-monooxygenase

hetero molecules

defined by author
Evidence: gel filtration
139 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Phenol 2-monooxygenase

D: Phenol 2-monooxygenase

hetero molecules

defined by author
139 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	175.169, 178.193, 124.721
Angle α, β, γ (deg.)	90.000, 129.301, 90.000
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A
3	2	A
4	2	A
5	3	A
6	3	A
7	4	A
8	4	A
9	5	A
10	5	A
11	6	A
12	6	A

NCS domain segments:

Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: ALA / End label comp-ID: ALA / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 5 - 606 / Label seq-ID: 5 - 606

Dom-ID	Component-ID	Ens-ID
1	1	1
2	1	1
3	2	2
4	2	2
5	3	3
6	3	3
7	4	4
8	4	4
9	5	5
10	5	5
11	6	6
12	6	6

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

#1: Protein	Phenol 2-monooxygenase Mass: 68961.828 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trametes versicolor (turkey-tail fungus) Gene: TRAPUB_13730 / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 421 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.73 Å³/Da / Density % sol: 54.95 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Structure Screen 1+2 from Molecular Dimensions condition E12 (10 % PEG 6000, 5% MPD, 0.1 M HEPES pH 7.5)

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 31, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9762 Å / Relative weight: 1
Reflection	Resolution: 2.408→107.884 Å / Num. obs: 78277 / % possible obs: 92.4 % / Redundancy: 5.2 % / CC_1/2: 0.973 / R_merge(I) obs: 0.28 / R_pim(I) all: 0.134 / Net I/σ(I): 4.1
Reflection shell	Resolution: 2.408→2.595 Å / Redundancy: 5 % / R_merge(I) obs: 0.951 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3915 / CC_1/2: 0.648 / R_pim(I) all: 0.464 / % possible all: 73

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0405	refinement
autoPROC		data reduction
STARANISO		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.41→107.884 Å / Cor.coef. F_o:F_c: 0.92 / Cor.coef. F_o:F_c free: 0.887 / SU B: 23.223 / SU ML: 0.248 / Cross valid method: FREE R-VALUE / ESU R Free: 0.32
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2255	3986	5.093 %
R_work	0.1918	74278	-
all	0.194	-	-
obs	-	78264	68.732 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 26.309 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.863 Å²	0 Å²	-0.405 Å²
2-	-	1.032 Å²	-0 Å²
3-	-	-	0.211 Å²

Refinement step

Cycle: LAST / Resolution: 2.41→107.884 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18676	0	212	421	19309

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	19381
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	18035
X-RAY DIFFRACTION	r_angle_refined_deg	1.491	1.649	26365
X-RAY DIFFRACTION	r_angle_other_deg	0.479	1.577	41506
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.121	5	2410
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	10.138	5	144
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	1.06	5	4
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.936	10	3066
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.874	10	891
X-RAY DIFFRACTION	r_chiral_restr	0.065	0.2	2875
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	22929
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	4479
X-RAY DIFFRACTION	r_nbd_refined	0.211	0.2	3722
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.195	0.2	16783
X-RAY DIFFRACTION	r_nbtor_refined	0.182	0.2	9500
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.083	0.2	10376
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.162	0.2	554
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.04	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.269	0.2	29
X-RAY DIFFRACTION	r_nbd_other	0.192	0.2	105
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.134	0.2	5
X-RAY DIFFRACTION	r_mcbond_it	1.761	1.539	9634
X-RAY DIFFRACTION	r_mcbond_other	1.761	1.539	9634
X-RAY DIFFRACTION	r_mcangle_it	2.981	2.759	12037
X-RAY DIFFRACTION	r_mcangle_other	2.981	2.76	12038
X-RAY DIFFRACTION	r_scbond_it	2.247	1.778	9747
X-RAY DIFFRACTION	r_scbond_other	2.242	1.778	9744
X-RAY DIFFRACTION	r_scangle_it	3.758	3.189	14325
X-RAY DIFFRACTION	r_scangle_other	3.758	3.19	14326
X-RAY DIFFRACTION	r_lrange_it	6.165	17.559	21506
X-RAY DIFFRACTION	r_lrange_other	6.165	17.567	21490
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.064	0.05	19364
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.059	0.05	19428
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.057	0.05	19524
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.063	0.05	19463
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.068	0.05	19344
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.065	0.05	19398

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.06415	0.0501
1	2	A	X-RAY DIFFRACTION	Local ncs	0.06415	0.0501
2	3	A	X-RAY DIFFRACTION	Local ncs	0.05907	0.0501
2	4	A	X-RAY DIFFRACTION	Local ncs	0.05907	0.0501
3	5	A	X-RAY DIFFRACTION	Local ncs	0.05719	0.0501
3	6	A	X-RAY DIFFRACTION	Local ncs	0.05719	0.0501
4	7	A	X-RAY DIFFRACTION	Local ncs	0.0629	0.0501
4	8	A	X-RAY DIFFRACTION	Local ncs	0.0629	0.0501
5	9	A	X-RAY DIFFRACTION	Local ncs	0.06825	0.0501
5	10	A	X-RAY DIFFRACTION	Local ncs	0.06825	0.0501
6	11	A	X-RAY DIFFRACTION	Local ncs	0.06467	0.0501
6	12	A	X-RAY DIFFRACTION	Local ncs	0.06467	0.0501

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.41-2.473	0.349	42	0.285	687	0.289	8371	0.929	0.946	8.7086	0.284
2.473-2.54	0.347	74	0.274	1438	0.277	8208	0.926	0.954	18.4211	0.268
2.54-2.614	0.345	109	0.276	2150	0.279	7943	0.92	0.952	28.4401	0.27
2.614-2.694	0.293	136	0.259	2663	0.26	7737	0.951	0.959	36.1768	0.252
2.694-2.783	0.286	138	0.268	3198	0.269	7497	0.942	0.955	44.4978	0.26
2.783-2.88	0.282	210	0.249	3770	0.25	7227	0.952	0.964	55.0713	0.238
2.88-2.989	0.286	274	0.243	4652	0.245	7037	0.949	0.963	70.0014	0.229
2.989-3.111	0.28	295	0.243	5457	0.245	6719	0.948	0.961	85.608	0.228
3.111-3.249	0.272	345	0.231	6030	0.233	6452	0.95	0.966	98.8066	0.217
3.249-3.407	0.254	347	0.218	5819	0.22	6170	0.958	0.971	99.9352	0.204
3.407-3.592	0.219	272	0.2	5622	0.201	5897	0.971	0.976	99.9491	0.19
3.592-3.809	0.218	265	0.188	5303	0.189	5570	0.97	0.979	99.9641	0.18
3.809-4.072	0.213	277	0.173	4947	0.175	5235	0.973	0.982	99.7899	0.167
4.072-4.397	0.196	263	0.153	4625	0.155	4889	0.976	0.986	99.9795	0.151
4.397-4.816	0.17	224	0.144	4256	0.145	4485	0.982	0.989	99.8885	0.145
4.816-5.384	0.176	198	0.143	3859	0.145	4057	0.982	0.989	100	0.144
5.384-6.214	0.185	193	0.144	3410	0.146	3604	0.98	0.989	99.9723	0.141
6.214-7.604	0.16	151	0.14	2876	0.141	3028	0.986	0.988	99.967	0.14
7.604-10.727	0.155	104	0.122	2261	0.124	2365	0.985	0.991	100	0.133
10.727-107.884	0.244	69	0.257	1253	0.257	1345	0.964	0.956	98.29	0.294

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	0.5457	0.0691	0.0963	0.6301	-0.0533	0.9124	-0.016	-0.0651	0.0919	0.0084	0.0022	-0.0669	-0.1213	0.0307	0.0137	0.0607	0.0115	0.0328	0.0152	-0.0007	0.0537	-5.6695	0.4622	48.6081
2	0.7504	-0.1405	-0.0526	0.5125	-0.173	0.6765	-0.0237	-0.0271	0.146	0.0517	0.0044	-0.0618	-0.0935	0.098	0.0193	0.0971	-0.02	0.0304	0.017	-0.0068	0.0513	42.2835	-1.9449	8.8649
3	0.4965	-0.0757	0.0867	0.6115	-0.0683	0.8902	0.0511	0.0264	-0.1426	-0.0133	-0.0086	0.0343	0.171	-0.0638	-0.0426	0.0747	-0.0121	0.0165	0.011	-0.0023	0.0801	-4.987	-40.9081	51.1361
4	0.694	-0.0786	-0.0739	0.7059	0.1131	0.5423	0.0066	0.0377	-0.1082	0.0098	0.0007	0.0135	0.0843	-0.0203	-0.0074	0.0796	0.0091	0.0248	0.0073	0.0044	0.0385	45.0832	-43.363	10.2007

Refinement TLS group

Selection: ALL

-
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

-
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

-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

-
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