PDB-8yp9: the crystal structure of wildtype Magnaporthe grisea oxidoreducta...

ID or keywords:

Entry

Database: PDB / ID: 8yp9

Title

the crystal structure of wildtype Magnaporthe grisea oxidoreductase in complex with NADP

Components

NADP-dependent oxidoreductase domain-containing protein

Keywords

OXIDOREDUCTASE / Magnaporthe oryzae / glycerol / turgor pressure

Function / homology

Function and homology information

oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / nucleotide binding
Similarity search - Function

Biological species

Pyricularia grisea (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 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	8yp9.cif.gz	399.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8yp9.ent.gz	331.1 KB	Display	PDB format
PDBx/mmJSON format	8yp9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8yp9_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	8yp9_full_validation.pdf.gz	1.3 MB	Display
Data in XML	8yp9_validation.xml.gz	49.9 KB	Display
Data in CIF	8yp9_validation.cif.gz	65.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yp/8yp9 ftp://data.pdbj.org/pub/pdb/validation_reports/yp/8yp9	HTTPS FTP

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Related structure data

Related structure data	8yp2C 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&software
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&software
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&software
38.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	64.617, 111.449, 171.840
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: 37582.398 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-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
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 482 / 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: 55.17 %
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: Apr 5, 2019

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.3→50 Å / Num. obs: 55459 / % possible obs: 99.3 % / Redundancy: 12.6 % / CC_1/2: 0.988 / CC star: 0.997 / R_merge(I) obs: 0.282 / R_pim(I) all: 0.082 / R_rim(I) all: 0.294 / Χ²: 0.952 / Net I/σ(I): 3.1 / Num. measured all: 697240

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
2.3-2.38	10.6	1.41	5272	0.749	0.925	0.43	1.477	0.861	95.8
2.38-2.48	11.8	1.367	5476	0.78	0.936	0.403	1.427	0.869	99.5
2.48-2.59	12.6	1.218	5500	0.868	0.964	0.352	1.269	0.866	99.8
2.59-2.73	12.7	0.947	5507	0.899	0.973	0.274	0.986	0.884	99.9
2.73-2.9	12	0.648	5506	0.938	0.984	0.194	0.677	0.91	99.7
2.9-3.12	13.7	0.458	5555	0.977	0.994	0.127	0.476	0.935	100
3.12-3.44	13.6	0.25	5574	0.991	0.998	0.07	0.26	0.998	100
3.44-3.93	13.1	0.153	5599	0.995	0.999	0.044	0.159	1.007	100
3.93-4.95	12.9	0.105	5656	0.996	0.999	0.03	0.11	1.026	99.6
4.95-50	12.7	0.087	5814	0.998	1	0.025	0.091	1.117	98.4

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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: 2.3→25.15 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.26 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2328	3691	3.6 %
R_work	0.1828	-	-
obs	0.1846	55459	96.44 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.3→25.15 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7642	0	144	482	8268

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	7989
X-RAY DIFFRACTION	f_angle_d	1.051	10891
X-RAY DIFFRACTION	f_dihedral_angle_d	14.422	1098
X-RAY DIFFRACTION	f_chiral_restr	0.054	1172
X-RAY DIFFRACTION	f_plane_restr	0.009	1401

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 (%)
2.3-2.33	0.2953	121	0.2868	3256	X-RAY DIFFRACTION	82
2.33-2.36	0.3648	137	0.2646	3528	X-RAY DIFFRACTION	90
2.36-2.4	0.3511	141	0.2635	3667	X-RAY DIFFRACTION	93
2.4-2.43	0.2985	141	0.2669	3667	X-RAY DIFFRACTION	94
2.43-2.47	0.3438	144	0.2507	3811	X-RAY DIFFRACTION	95
2.47-2.51	0.2899	139	0.25	3672	X-RAY DIFFRACTION	94
2.51-2.55	0.2834	137	0.2453	3775	X-RAY DIFFRACTION	96
2.55-2.6	0.2928	131	0.2395	3765	X-RAY DIFFRACTION	95
2.6-2.65	0.3479	137	0.2361	3803	X-RAY DIFFRACTION	96
2.65-2.7	0.2872	141	0.2327	3796	X-RAY DIFFRACTION	96
2.7-2.76	0.2542	145	0.2268	3796	X-RAY DIFFRACTION	97
2.76-2.83	0.3454	146	0.2199	3830	X-RAY DIFFRACTION	97
2.83-2.9	0.2401	141	0.2106	3847	X-RAY DIFFRACTION	98
2.9-2.98	0.2732	143	0.2106	3864	X-RAY DIFFRACTION	98
2.98-3.06	0.2991	146	0.2049	3903	X-RAY DIFFRACTION	98
3.06-3.16	0.3174	145	0.2015	3827	X-RAY DIFFRACTION	98
3.16-3.28	0.2453	143	0.167	3894	X-RAY DIFFRACTION	99
3.28-3.41	0.2043	147	0.1608	3941	X-RAY DIFFRACTION	99
3.41-3.56	0.2071	140	0.1618	3901	X-RAY DIFFRACTION	99
3.56-3.75	0.1811	146	0.1417	3894	X-RAY DIFFRACTION	99
3.75-3.98	0.1895	146	0.1359	3908	X-RAY DIFFRACTION	99
3.98-4.29	0.1959	142	0.1297	3917	X-RAY DIFFRACTION	99
4.29-4.72	0.1445	146	0.1243	3888	X-RAY DIFFRACTION	100
4.72-5.39	0.1639	156	0.1439	3954	X-RAY DIFFRACTION	99
5.39-6.77	0.1965	142	0.1792	3872	X-RAY DIFFRACTION	99
6.78-25.15	0.192	148	0.1717	3852	X-RAY DIFFRACTION	97

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	0.9305	-0.9601	0.4805	2.6549	0.2418	2.2557	-0.1481	-0.0112	0.0896	0.0015	0.1462	0.1248	-0.1216	-0.0456	0.0271	0.1377	0.0123	0.0282	0.2074	0.023	0.1645	54.8567	67.212	26.8812
2	1.6758	-0.433	0.0068	1.041	-0.5725	1.465	-0.1009	-0.1178	-0.1638	0.0493	-0.0006	-0.1495	0.1341	0.0976	0.0906	0.1708	0.0075	0.0171	0.1486	0.0544	0.2274	66.0254	56.1823	31.4441
3	1.0316	-1.0318	0.688	1.1479	-0.664	1.7067	0.0262	0.4759	0.208	-0.0443	-0.3695	-0.5124	0.0432	1.0216	0.0943	0.1954	-0.0375	0.0013	0.3651	0.0277	0.2703	61.7129	67.3644	9.5249
4	0.9757	-0.0091	0.8531	1.3025	-0.4662	1.4714	0.0111	0.2839	-0.1302	-0.2179	-0.0759	-0.1175	0.1743	0.0914	0.0528	0.228	-0.0202	0.0437	0.2037	0.0023	0.1808	62.3761	62.4403	12.7879
5	2.0002	-0.2521	-1	2.0705	-0.343	1.2725	-0.12	0.0312	-0.1887	-0.1825	-0.0798	0.3905	0.255	-0.3161	0.1256	0.2898	-0.0319	-0.0067	0.3263	-0.0266	0.25	73.4837	50.4857	80.4815
6	1.3508	-0.0675	-0.4761	1.535	0.175	1.7682	0.0062	-0.0394	0.2559	0.1273	0.0909	0.1748	-0.2165	-0.1322	-0.0818	0.2287	0.0019	-0.0092	0.2078	0.0069	0.2502	65.3165	59.1704	75.9482
7	1.1573	-0.4508	0.135	0.4914	-0.0946	0.9877	-0.0456	0.1899	0.3186	-0.0635	-0.0033	-0.0868	-0.1891	0.1737	0.04	0.2336	-0.0383	-0.0187	0.2073	0.0765	0.2491	78.2059	56.7222	63.937
8	0.1531	-0.2543	-0.2801	3.7891	-0.0796	1.1118	-0.2508	0.2834	0.1109	-0.6533	0.1807	0.6716	0.2189	-0.2253	0.0164	0.2725	-0.0117	-0.061	0.3728	0.0568	0.268	72.0236	38.8273	70.0654
9	0.4657	0.1294	0.0841	1.1956	-0.292	1.0666	0.0111	-0.041	-0.0621	0.1586	-0.0985	0.0476	0.1222	-0.1652	0.0732	0.2256	-0.0296	0.0093	0.2311	0.0101	0.1677	76.8031	34.8698	79.3657
10	1.4612	-1.8531	0.5336	3.4574	-1.1945	0.4751	0.1677	0.7514	0.0516	-0.8752	-0.0088	0.2557	0.055	0.0668	-0.0149	0.2835	-0.0318	-0.064	0.3386	0.0352	0.2455	71.6002	43.9427	57.5566
11	0.826	0.1827	-0.1538	2.6276	-0.4946	1.6775	-0.1606	0.0926	-0.1369	-0.053	0.1798	-0.2875	0.0236	0.2436	-0.0108	0.1947	-0.0558	-0.0194	0.3428	-0.048	0.2661	35.4563	22.9677	58.3775
12	1.6815	-0.3488	0.2753	1.5298	0.4297	1.2078	-0.3059	0.6547	-0.0776	-0.6305	0.3852	-0.4511	-0.0223	0.1175	-0.0225	0.2975	-0.1526	0.1156	0.4975	-0.1175	0.2145	40.8861	27.5723	45.1451
13	1.554	0.2394	-0.392	1.6739	-0.1706	2.614	-0.0727	0.2777	0.0982	-0.1755	0.0124	-0.1644	-0.099	0.6614	0.0358	0.1851	-0.0678	-0.0133	0.248	0.0207	0.2195	40.1059	39.5702	63.3103
14	1.5159	0.5251	0.1867	0.9675	0.9794	1.277	-0.0176	0.0893	-0.1124	0.0234	0.0574	-0.2589	-0.1168	0.2119	-0.0274	0.1791	0.0118	-0.0278	0.152	0.0312	0.2186	40.7463	36.413	67.025

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 46 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 47 through 214 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 215 through 253 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 254 through 326 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 5 through 34 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 35 through 134 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 135 through 214 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 215 through 240 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 241 through 302 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 303 through 322 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 4 through 59 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 60 through 176 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 177 through 253 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 254 through 324 )

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