PDB-8yp2: the crystal structure of inactive Magnaporthe grisea oxidoreducta...

ID or keywords:

Entry

Database: PDB / ID: 8yp2

Title

the crystal structure of inactive Magnaporthe grisea oxidoreductase in complex with NADP and Glycerol

Components

NADP-dependent oxidoreductase domain-containing protein

Keywords

OXIDOREDUCTASE / Magnaporthe oryzae / glycerol / turgor pressure

Function / homology

Function and homology information

oxidoreductase activity
Similarity search - Function

Biological species

Pyricularia grisea (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.91 Å

Authors

Huang, X. / Jiang, H. / Tang, D. / Lin, S.

Funding support

China, 1items

Citation

Journal: Plant Pathol J / Year: 2025
Title: Crystal Structure of an Aldo-keto Reductase MGG_00097 from Magnaporthe grisea.
Authors: Huang, X. / Jiang, H. / Lin, Y. / Li, X. / Bi, C. / Qi, S. / Tang, D. / Wang, Z. / Lin, S.

History

Deposition	Mar 15, 2024	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Mar 19, 2025	Provider: repository / Type: Initial release
Revision 1.1	Apr 23, 2025	Group: Database references / Category: citation / citation_author Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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	8yp2.cif.gz	390.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8yp2.ent.gz	324.4 KB	Display	PDB format
PDBx/mmJSON format	8yp2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8yp2_validation.pdf.gz	1.9 MB	Display	wwPDB validaton report
Full document	8yp2_full_validation.pdf.gz	1.9 MB	Display
Data in XML	8yp2_validation.xml.gz	44.1 KB	Display
Data in CIF	8yp2_validation.cif.gz	55 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yp/8yp2 ftp://data.pdbj.org/pub/pdb/validation_reports/yp/8yp2	HTTPS FTP

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Related structure data

Related structure data	8yp9C C: citing same article (ref.)
Similar structure data	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	#92 - Aug 2007 Anabolic Steroids similarity (7)

Deposited unit

A: NADP-dependent oxidoreductase domain-containing protein

B: NADP-dependent oxidoreductase domain-containing protein

C: NADP-dependent oxidoreductase domain-containing protein

hetero molecules

115 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: NADP-dependent oxidoreductase domain-containing protein

hetero molecules

defined by author
Evidence: gel filtration
38.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: NADP-dependent oxidoreductase domain-containing protein

hetero molecules

defined by author
38.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: NADP-dependent oxidoreductase domain-containing protein

hetero molecules

defined by author
38.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	64.761, 110.780, 171.508
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	NADP-dependent oxidoreductase domain-containing protein Mass: 37490.305 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyricularia grisea (fungus) / Gene: PgNI_11595 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6P8AP13
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE Mass: 743.405 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂₁H₂₈N₇O₁₇P₃ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.74 Å³/Da / Density % sol: 55.03 %
Crystal grow	Temperature: 291 K / Method: evaporation Details: 0.2M NaCl, 2% ethyl acetate, 1.2M NaH2PO4, and 1.2M K2HPO4

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL19U1 / Wavelength: 1 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 11, 2019

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.9→50 Å / Num. obs: 27660 / % possible obs: 98.8 % / Redundancy: 7.9 % / CC_1/2: 0.921 / CC star: 0.979 / R_merge(I) obs: 0.395 / R_pim(I) all: 0.145 / R_rim(I) all: 0.422 / Χ²: 0.497 / Net I/σ(I): 2 / Num. measured all: 217408

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.9-2.95	6.5	1.325	1297	0.427	0.774	0.549	1.44	0.505	94.9
2.95-3	6.8	1.343	1316	0.524	0.829	0.54	1.453	0.431	96.3
3-3.06	6.9	1.251	1355	0.624	0.877	0.492	1.348	0.433	97.8
3.06-3.12	7	1.101	1305	0.686	0.902	0.434	1.188	0.426	95.4
3.12-3.19	7.5	0.913	1334	0.867	0.964	0.343	0.978	0.439	98
3.19-3.27	7.8	0.756	1384	0.896	0.972	0.278	0.807	0.434	98.7
3.27-3.35	7.9	0.644	1373	0.937	0.984	0.236	0.687	0.44	100
3.35-3.44	7.9	0.604	1366	0.926	0.981	0.219	0.643	0.439	99.1
3.44-3.54	8	0.546	1380	0.945	0.986	0.198	0.582	0.454	99.9
3.54-3.65	7.9	0.483	1379	0.948	0.986	0.176	0.515	0.451	99.2
3.65-3.78	7.5	0.394	1400	0.955	0.989	0.15	0.423	0.505	99.9
3.78-3.94	8.3	0.375	1349	0.97	0.992	0.134	0.399	0.485	99.4
3.94-4.11	8.5	0.327	1410	0.978	0.995	0.115	0.347	0.477	99.6
4.11-4.33	8.6	0.294	1389	0.986	0.996	0.104	0.312	0.497	99.6
4.33-4.6	8.3	0.255	1406	0.986	0.997	0.092	0.271	0.524	100
4.6-4.96	8	0.234	1388	0.985	0.996	0.085	0.25	0.526	98.9
4.96-5.46	8.9	0.306	1404	0.984	0.996	0.105	0.324	0.506	99.7
5.46-6.24	8.7	0.341	1428	0.982	0.995	0.119	0.361	0.502	99.9
6.24-7.86	8.3	0.239	1453	0.986	0.997	0.086	0.255	0.547	99.9
7.86-50	7.7	0.102	1544	0.996	0.999	0.038	0.109	0.849	99.3

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
HKL-2000		data scaling
HKL-2000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.91→46.83 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.1 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2485	1947	7.28 %
R_work	0.2025	-	-
obs	0.2059	26731	95.6 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.91→46.83 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7609	0	162	4	7775

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	7973
X-RAY DIFFRACTION	f_angle_d	1.207	10863
X-RAY DIFFRACTION	f_dihedral_angle_d	14.787	1101
X-RAY DIFFRACTION	f_chiral_restr	0.052	1170
X-RAY DIFFRACTION	f_plane_restr	0.01	1397

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.91-2.98	0.3779	128	0.3103	1584	X-RAY DIFFRACTION	87
2.98-3.06	0.3638	132	0.296	1669	X-RAY DIFFRACTION	91
3.06-3.15	0.3066	126	0.2632	1637	X-RAY DIFFRACTION	91
3.15-3.25	0.293	137	0.2411	1737	X-RAY DIFFRACTION	94
3.25-3.37	0.2763	139	0.2202	1743	X-RAY DIFFRACTION	97
3.37-3.5	0.2866	138	0.2254	1762	X-RAY DIFFRACTION	96
3.5-3.66	0.2545	141	0.2016	1778	X-RAY DIFFRACTION	97
3.66-3.85	0.2615	139	0.1882	1782	X-RAY DIFFRACTION	97
3.85-4.09	0.2183	139	0.1781	1805	X-RAY DIFFRACTION	98
4.09-4.41	0.2136	144	0.1616	1822	X-RAY DIFFRACTION	99
4.41-4.85	0.1925	144	0.1525	1824	X-RAY DIFFRACTION	98
4.85-5.55	0.2225	142	0.177	1826	X-RAY DIFFRACTION	97
5.55-6.99	0.2132	147	0.1972	1855	X-RAY DIFFRACTION	98
7-46.83	0.2237	151	0.2054	1960	X-RAY DIFFRACTION	98

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	2.6798	0.0613	-0.9194	2.9336	0.0558	1.8883	0.0004	-0.2471	0.1158	0.1443	-0.0076	0.0015	-0.1424	-0.0583	0.0329	0.2139	0.0101	-0.0236	0.2593	0.0393	0.2242	59.3841	64.7357	32.5443
2	2.1588	0.1797	-0.0167	0.9269	-0.1083	2.3698	0.0168	-0.0861	-0.4008	-0.072	0.0333	-0.2756	0.2672	0.1061	-0.0572	0.2385	0.0458	0.051	0.2104	0.0506	0.2995	68.6412	50.8414	28.0752
3	3.2926	-1.7127	0.6523	3.2054	0.0695	4.2449	-0.537	0.9473	0.6064	-0.9094	0.0651	-1.2379	-0.3764	0.2934	0.4171	0.4597	0.0097	0.01	0.6256	-0.0202	0.5385	66.546	63.2524	13.7039
4	1.3498	-0.2501	0.6757	0.6836	-0.6897	1.6309	0.0742	0.1621	-0.2228	-0.0755	-0.0614	-0.0735	0.0827	0.0865	-0.0006	0.207	0.0036	0.0361	0.2442	0.0383	0.2184	61.2422	63.5429	11.1241
5	2.8283	0.2897	-1.6984	2.2129	-1.1841	1.3582	-0.0364	-0.2589	0.0309	0.1072	0.0171	0.1731	-0.1177	-0.4865	-0.05	0.2877	-0.0162	-0.0192	0.4657	0.0008	0.1383	70.2612	50.185	81.5743
6	2.2788	0.2184	-0.3523	0.8772	-0.6604	2.0376	-0.0128	0.1211	0.387	0.0066	0.0826	0.0263	-0.3703	0.1171	0.0141	0.2441	0.0046	-0.0101	0.2916	0.0017	0.1936	71.8164	58.4164	69.4711
7	0.9392	0.7105	-0.4633	4.9505	-0.5583	1.5441	-0.2655	0.3412	-0.0374	-0.1664	0.1768	0.2868	0.0767	-0.3408	0.0517	0.1804	-0.0054	-0.0116	0.4087	0.0107	0.18	75.0861	35.2114	74.9821
8	0.2056	-0.704	0.2478	2.0204	0.1685	0.717	-0.0777	0.0855	-0.0101	-0.0052	0.0278	-0.0067	0.2253	0.1888	0.0434	0.2075	-0.0375	0.0055	0.4009	0.0399	0.1919	74.9431	39.2894	71.0359
9	0.9371	-0.1272	0.7984	3.2418	-1.0069	3.5076	-0.1969	0.1497	-0.5508	-0.3958	0.1192	-0.5339	0.4432	-0.6433	0.0381	0.346	-0.0608	-0.0001	0.4601	0.0053	0.4628	32.6597	26.2954	58.7048
10	1.7239	0.9172	0.864	2.1393	0.9331	0.8979	-0.4453	0.6837	-0.3566	-0.7895	0.5484	-0.6743	-0.0508	0.204	0.0395	0.4244	-0.1808	0.1669	0.6779	-0.1673	0.381	40.6258	25.6596	47.2226
11	1.887	0.2042	-0.4107	2.9692	-0.8702	5.0086	-0.0717	0.2152	0.2751	-0.1896	0.1958	-0.0486	0.0699	0.3142	-0.1007	0.1572	-0.0553	0.0055	0.309	-0.025	0.2187	39.2241	38.694	63.9061
12	2.0686	1.1329	0.1479	1.0916	1.031	1.1331	-0.0446	0.2027	0.1254	0.0404	0.0909	-0.2645	-0.0786	0.1013	-0.0202	0.2027	0.0655	-0.0197	0.3316	0.0375	0.2721	42.1753	36.3141	66.2583

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 109 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 110 through 214 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 215 through 236 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 237 through 326 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 5 through 46 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 47 through 214 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 215 through 265 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 266 through 322 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 4 through 34 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 35 through 176 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 177 through 265 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 266 through 324 )

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