PDB-9ou1: Crystal structure of maize AKR4C13 in P21 space group

ID or keywords:

Entry

Database: PDB / ID: 9ou1

Title

Crystal structure of maize AKR4C13 in P21 space group

Components

Aldose reductase, AKR4C13

Keywords

OXIDOREDUCTASE / aldo-keto reductase superfamily / AKR4C subfamily

Function / homology

Function and homology information

oxidoreductase activity / nucleotide binding
Similarity search - Function

Biological species

Zea mays (maize)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.45 Å

Authors

Santos, M.L. / Giuseppe, P.O. / Kiyota, E. / Schmelz, E.A. / Yunes, J.A. / Koch, K.E. / Murakami, M.T. / Aparicio, R. / Sousa, S.M.

Funding support

United States, 1items

Citation

Journal: J.Biol.Chem. / Year: 2025
Title: Functional Genomics and Structural Insights into Maize Aldo-Keto Reductase-4 Family: Stress Metabolism and Substrate Specificity in Embryos.
Authors: Morais de Sousa, S. / Oliveira de Giuseppe, P. / Murakami, M.T. / Guan, J.C. / Saunders, J.W. / Kiyota, E. / Santos, M.L. / Schmelz, E.A. / Yunes, J.A. / Koch, K.E.

History

Deposition	May 28, 2025	Deposition site: RCSB / Processing site: RCSB
Supersession	Jul 2, 2025	ID: 5JGY
Revision 1.0	Jul 2, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9ou1.cif.gz	160 KB	Display	PDBx/mmCIF format
PDB format	pdb9ou1.ent.gz	120.4 KB	Display	PDB format
PDBx/mmJSON format	9ou1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ou/9ou1 ftp://data.pdbj.org/pub/pdb/validation_reports/ou/9ou1	HTTPS FTP

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Related structure data

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: Aldose reductase, AKR4C13

B: Aldose reductase, AKR4C13

hetero molecules

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

1

A: Aldose reductase, AKR4C13

hetero molecules

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

2

B: Aldose reductase, AKR4C13

hetero molecules

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

Unit cell

Length a, b, c (Å)	53.823, 115.370, 56.532
Angle α, β, γ (deg.)	90.000, 104.247, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Aldose reductase, AKR4C13 / Uncharacterized protein Mass: 36767.895 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zea mays (maize) / Gene: AR3 / Production host: Escherichia coli (E. coli) / References: UniProt: E9JVD4
#2: Chemical	ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₂₈N₇O₁₇P₃ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 695 / Source method: isolated from a natural source / Formula: H₂O
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: 2.31 Å³/Da / Density % sol: 46.72 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion Details: 15% (w/v) PEG 1500 and 0.1 M SPG buffer pH 4.5 added by 0.01 M of beta-NADP+

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
Detector	Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 9, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9334 Å / Relative weight: 1
Reflection	Resolution: 1.45→57.65 Å / Num. obs: 120277 / % possible obs: 98.6 % / Redundancy: 1.9 % / R_merge(I) obs: 0.048 / Net I/σ(I): 11.37
Reflection shell	Resolution: 1.45→1.54 Å / R_merge(I) obs: 0.644 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 19245 / % possible all: 98.6

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430	refinement
PDB_EXTRACT		data extraction
XDS		data reduction
XSCALE		data scaling
BALBES		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.45→39.728 Å / Cor.coef. F_o:F_c: 0.971 / Cor.coef. F_o:F_c free: 0.964 / SU B: 1.216 / SU ML: 0.045 / Cross valid method: FREE R-VALUE / ESU R: 0.06 / ESU R Free: 0.061
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.183	5905	5.008 %
R_work	0.1592	112014	-
all	0.16	-	-
obs	-	117919	99.953 %

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: 15.675 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.041 Å²	-0 Å²	-0.062 Å²
2-	-	-0.057 Å²	-0 Å²
3-	-	-	0.042 Å²

Refinement step

Cycle: LAST / Resolution: 1.45→39.728 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4848	0	140	695	5683

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.012	5231
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	4951
X-RAY DIFFRACTION	r_angle_refined_deg	1.854	1.851	7087
X-RAY DIFFRACTION	r_angle_other_deg	0.64	1.786	11441
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.182	5	637
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	7.592	5	41
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	2.157	5	4
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.88	10	905
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.793	10	233
X-RAY DIFFRACTION	r_chiral_restr	0.09	0.2	762
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	6132
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	1154
X-RAY DIFFRACTION	r_nbd_refined	0.223	0.2	1112
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.198	0.2	4529
X-RAY DIFFRACTION	r_nbtor_refined	0.18	0.2	2433
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.08	0.2	2507
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.166	0.2	464
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.184	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.245	0.2	15
X-RAY DIFFRACTION	r_nbd_other	0.236	0.2	49
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.157	0.2	34
X-RAY DIFFRACTION	r_mcbond_it	1.547	1.491	2518
X-RAY DIFFRACTION	r_mcbond_other	1.543	1.491	2518
X-RAY DIFFRACTION	r_mcangle_it	2.233	2.682	3162
X-RAY DIFFRACTION	r_mcangle_other	2.235	2.682	3163
X-RAY DIFFRACTION	r_scbond_it	2.891	1.786	2713
X-RAY DIFFRACTION	r_scbond_other	2.89	1.786	2714
X-RAY DIFFRACTION	r_scangle_it	4.462	3.096	3924
X-RAY DIFFRACTION	r_scangle_other	4.461	3.096	3925
X-RAY DIFFRACTION	r_lrange_it	5.823	19.321	6089
X-RAY DIFFRACTION	r_lrange_other	5.714	19.218	6004

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
1.45-1.488	0.307	427	0.289	8268	0.29	8697	0.935	0.94	99.977	0.276
1.488-1.528	0.254	395	0.252	8096	0.252	8500	0.953	0.953	99.8941	0.234
1.528-1.573	0.236	405	0.224	7839	0.225	8244	0.963	0.964	100	0.203
1.573-1.621	0.226	373	0.211	7591	0.212	7971	0.964	0.968	99.9122	0.188
1.621-1.674	0.22	417	0.188	7358	0.19	7776	0.967	0.976	99.9871	0.164
1.674-1.733	0.209	394	0.173	7113	0.175	7510	0.97	0.98	99.9601	0.149
1.733-1.798	0.202	362	0.158	6876	0.16	7238	0.973	0.984	100	0.135
1.798-1.871	0.195	330	0.147	6646	0.149	6982	0.976	0.986	99.9141	0.13
1.871-1.954	0.174	365	0.144	6339	0.145	6704	0.981	0.987	100	0.127
1.954-2.049	0.168	334	0.145	6074	0.147	6411	0.982	0.987	99.9532	0.133
2.049-2.16	0.176	325	0.142	5767	0.144	6093	0.982	0.988	99.9836	0.131
2.16-2.29	0.176	306	0.14	5432	0.142	5739	0.981	0.988	99.9826	0.131
2.29-2.448	0.169	275	0.129	5186	0.131	5463	0.984	0.99	99.9634	0.123
2.448-2.643	0.169	237	0.136	4776	0.138	5014	0.983	0.988	99.9801	0.132
2.643-2.894	0.155	210	0.137	4433	0.138	4643	0.985	0.988	100	0.136
2.894-3.234	0.171	221	0.151	4002	0.152	4227	0.982	0.986	99.9054	0.153
3.234-3.73	0.162	179	0.148	3543	0.148	3723	0.986	0.988	99.9731	0.155
3.73-4.558	0.141	164	0.134	3000	0.134	3165	0.988	0.99	99.9684	0.15
4.558-6.404	0.183	119	0.166	2343	0.167	2462	0.986	0.989	100	0.187
6.404-39.728	0.23	67	0.208	1332	0.209	1406	0.981	0.977	99.5021	0.238

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