PDB-8s6s: Oxidoreductase from Phytophthora sojae

ID or keywords:

Entry

Database: PDB / ID: 8s6s

Title

Oxidoreductase from Phytophthora sojae

Components

Mucin-like protein

Keywords

OXIDOREDUCTASE / LPMO / AA17 / Phytophthora sojae / phytopathogen

Function / homology

COPPER (II) ION / Mucin-like protein

Function and homology information

Biological species

Phytophthora sojae (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.789 Å

Authors

Banerjee, S. / Turella, S. / Morth, J.P. / Abou Hachem, M.

Funding support

Denmark, 1items

Citation

Journal: Nat Commun / Year: 2025
Title: Enzymatic oxidation of galacturonides from pectin breakdown contributes to stealth infection by Oomycota phytopathogens.
Authors: Turella, S. / He, C. / Zhao, L. / Banerjee, S. / Plouhinec, L. / Assiah Yao, R. / Norgaard Kejlstrup, M.C. / Grisel, S. / So, Y. / Annic, B. / Fanuel, M. / Haddad Momeni, M. / Bissaro, B. / ...

History

Deposition	Feb 28, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 12, 2025	Provider: repository / Type: Initial release
Revision 1.1	May 14, 2025	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

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Download

PDBx/mmCIF format	8s6s.cif.gz	98 KB	Display	PDBx/mmCIF format
PDB format	pdb8s6s.ent.gz	68.9 KB	Display	PDB format
PDBx/mmJSON format	8s6s.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8s6s_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	8s6s_full_validation.pdf.gz	1.2 MB	Display
Data in XML	8s6s_validation.xml.gz	22.3 KB	Display
Data in CIF	8s6s_validation.cif.gz	31.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s6/8s6s ftp://data.pdbj.org/pub/pdb/validation_reports/s6/8s6s	HTTPS FTP

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Related structure data

Related structure data	8s6gC 8s71C 9ffeC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Mucin-like protein

B: Mucin-like protein

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	46.267, 73.129, 116.418
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 2 molecules AB

#1: Protein	Mucin-like protein Mass: 20307.682 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Phytophthora sojae (eukaryote) / Gene: PHYSODRAFT_483955 / Production host: Escherichia coli (E. coli) / References: UniProt: G4YSM3

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Non-polymers , 5 types, 373 molecules

#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-CU / COPPER (II) ION Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: SO₄
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 366 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
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: 2.57 Å³/Da / Density % sol: 52.19 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 0.2 M Lithium sulfate, 0.1 M Tris pH 8.5, 30% w/v PEG 4000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.98 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 12, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 1.789→61.925 Å / Num. obs: 38093 / % possible obs: 100 % / Redundancy: 13.3 % / CC_1/2: 0.998 / Net I/σ(I): 16.3
Reflection shell	Resolution: 1.789→1.82 Å / Num. unique obs: 1838 / CC_1/2: 0.829

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0419	refinement
AutoProcess		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.789→61.925 Å / Cor.coef. F_o:F_c: 0.971 / Cor.coef. F_o:F_c free: 0.954 / SU B: 2.318 / SU ML: 0.072 / Cross valid method: FREE R-VALUE / ESU R: 0.107 / ESU R Free: 0.109
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2023	1905	5.001 %
R_work	0.1608	36188	-
all	0.163	-	-
obs	-	38093	99.974 %

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: 27.585 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.746 Å²	-0 Å²	0 Å²
2-	-	-1.326 Å²	0 Å²
3-	-	-	0.58 Å²

Refinement step

Cycle: LAST / Resolution: 1.789→61.925 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2686	0	26	366	3078

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.012	2890
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2555
X-RAY DIFFRACTION	r_angle_refined_deg	1.56	1.658	3947
X-RAY DIFFRACTION	r_angle_other_deg	0.558	1.594	5963
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.218	5	372
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	4.984	5	8
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.028	10	448
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.198	10	126
X-RAY DIFFRACTION	r_chiral_restr	0.088	0.2	400
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	3479
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	629
X-RAY DIFFRACTION	r_nbd_refined	0.218	0.2	532
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.204	0.2	2327
X-RAY DIFFRACTION	r_nbtor_refined	0.185	0.2	1393
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.086	0.2	1471
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.203	0.2	296
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.031	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined	0.055	0.2	4
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.102	0.2	11
X-RAY DIFFRACTION	r_nbd_other	0.149	0.2	45
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.117	0.2	17
X-RAY DIFFRACTION	r_mcbond_it	2.893	2.747	1449
X-RAY DIFFRACTION	r_mcbond_other	2.893	2.748	1449
X-RAY DIFFRACTION	r_mcangle_it	4.144	4.911	1831
X-RAY DIFFRACTION	r_mcangle_other	4.144	4.915	1832
X-RAY DIFFRACTION	r_scbond_it	4.634	3.188	1441
X-RAY DIFFRACTION	r_scbond_other	4.591	3.169	1434
X-RAY DIFFRACTION	r_scangle_it	7.111	5.565	2115
X-RAY DIFFRACTION	r_scangle_other	7.072	5.532	2104
X-RAY DIFFRACTION	r_lrange_it	8.645	29.984	3371
X-RAY DIFFRACTION	r_lrange_other	8.637	29.526	3286

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
1.789-1.835	0.276	125	0.228	2630	0.23	2755	0.95	0.963	100	0.216
1.835-1.885	0.203	140	0.197	2566	0.197	2707	0.969	0.972	99.9631	0.181
1.885-1.94	0.218	124	0.181	2503	0.183	2627	0.969	0.977	100	0.163
1.94-2	0.205	161	0.169	2390	0.171	2551	0.974	0.982	100	0.151
2-2.065	0.199	137	0.16	2347	0.162	2484	0.974	0.984	100	0.141
2.065-2.138	0.203	113	0.163	2277	0.165	2390	0.967	0.983	100	0.145
2.138-2.218	0.236	119	0.159	2239	0.162	2358	0.966	0.984	100	0.141
2.218-2.309	0.197	100	0.154	2123	0.156	2224	0.976	0.985	99.955	0.136
2.309-2.411	0.21	108	0.147	2059	0.15	2168	0.973	0.987	99.9539	0.131
2.411-2.529	0.188	90	0.138	1940	0.14	2030	0.981	0.989	100	0.122
2.529-2.665	0.21	109	0.147	1872	0.15	1981	0.977	0.987	100	0.134
2.665-2.827	0.223	101	0.162	1752	0.165	1854	0.969	0.984	99.9461	0.151
2.827-3.021	0.222	87	0.175	1683	0.177	1771	0.97	0.981	99.9435	0.168
3.021-3.263	0.225	70	0.183	1579	0.185	1649	0.974	0.982	100	0.18
3.263-3.573	0.179	73	0.17	1443	0.17	1516	0.982	0.985	100	0.17
3.573-3.993	0.171	62	0.146	1313	0.147	1376	0.982	0.989	99.9273	0.152
3.993-4.608	0.149	66	0.128	1183	0.129	1251	0.987	0.991	99.8401	0.141
4.608-5.636	0.22	51	0.142	1005	0.145	1056	0.978	0.99	100	0.161
5.636-7.937	0.196	47	0.177	798	0.178	845	0.977	0.985	100	0.198
7.937-61.925	0.294	22	0.202	486	0.205	510	0.927	0.971	99.6078	0.243

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