PDB-7s5i: Crystal structure of Aldose-6-phosphate reductase (Ald6PRase) fro...

ID or keywords:

Entry

Database: PDB / ID: 7s5i

Title

Crystal structure of Aldose-6-phosphate reductase (Ald6PRase) from peach (Prunus persica) leaves

Components

Sorbitol-6-phosphate dehydrogenase

Keywords

OXIDOREDUCTASE / aldo/keto reductase superfamily / aldose-6-phosphate reductase / Apium graveolens /

celery / mannose-6-phosphate reductase /

peach / Prunus persica

Function / homology

Function and homology information

aldose-6-phosphate reductase (NADPH) /

aldose-6-phosphate reductase (NADPH) activity /

D-threo-aldose 1-dehydrogenase activity / aldose reductase (NADPH) activity /

cytosol
Similarity search - Function

Biological species

Prunus persica (peach)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.61 Å

Authors

Zheng, Y. / Bhayani, J.A. / Romina, I.M. / Hartman, M.D. / Cereijo, A.E. / Ballicora, M.A. / Iglesias, A.A. / Figueroa, C.M. / Liu, D.

Funding support

United States, 1items

Citation

Journal: Plant Cell.Physiol. / Year: 2022
Title: Structural Determinants of Sugar Alcohol Biosynthesis in Plants: The Crystal Structures of Mannose-6-Phosphate and Aldose-6-Phosphate Reductases.
Authors: Minen, R.I. / Bhayani, J.A. / Hartman, M.D. / Cereijo, A.E. / Zheng, Y. / Ballicora, M.A. / Iglesias, A.A. / Liu, D. / Figueroa, C.M.

History

Deposition	Sep 10, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 16, 2022	Provider: repository / Type: Initial release
Revision 1.1	Mar 23, 2022	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	May 25, 2022	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7s5i.cif.gz	271.8 KB	Display	PDBx/mmCIF format
PDB format	pdb7s5i.ent.gz	218.1 KB	Display	PDB format
PDBx/mmJSON format	7s5i.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s5/7s5i ftp://data.pdbj.org/pub/pdb/validation_reports/s5/7s5i	HTTPS FTP

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Related structure data

Related structure data	7s5fC 1hqtS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7s5f-2 6z5h-1 6z5h-2 6kdf-4 4yzo-1 2oga-2 3bwo-3 1ye6-1 5z6u-d 1rlc-d Search similar-shape structures by Omokage search (details) 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 (8)

Deposited unit

A: Sorbitol-6-phosphate dehydrogenase

B: Sorbitol-6-phosphate dehydrogenase

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	178.360, 50.049, 82.506
Angle α, β, γ (deg.)	90.000, 111.770, 90.000
Int Tables number	5
Space group name H-M	C121

#1: Protein	Sorbitol-6-phosphate dehydrogenase / Aldose-6-phosphate reductase Mass: 34869.180 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Prunus persica (peach) / Gene: PRUPE_8G083400, PRUPE_ppa009007mg / Production host: Escherichia coli (E. coli) References: UniProt: A5JUQ9, aldose-6-phosphate reductase (NADPH)
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 859 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.45 Å³/Da / Density % sol: 49.84 %
Crystal grow	Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES and 20% (w/v) PEG 8000

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 1.008 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 15, 2019

Radiation

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

Radiation wavelength

Wavelength: 1.008 Å / Relative weight: 1

Reflection

Resolution: 1.61→50 Å / Num. obs: 86724 / % possible obs: 99 % / Redundancy: 7.2 % / B_iso Wilson estimate: 12.36 Å² / R_merge(I) obs: 0.057 / R_pim(I) all: 0.023 / R_rim(I) all: 0.062 / Χ²: 0.946 / Net I/σ(I): 11.6 / Num. measured all: 624800

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.61-1.64	7.1	0.4	4277	0.953	0.159	0.431	0.84	98.5
1.64-1.67	7.4	0.356	4298	0.962	0.139	0.382	0.847	98.8
1.67-1.7	7.3	0.301	4273	0.972	0.118	0.324	0.887	98.9
1.7-1.73	7.4	0.255	4327	0.978	0.1	0.274	0.92	98.9
1.73-1.77	7.3	0.222	4285	0.979	0.087	0.239	0.938	99
1.77-1.81	7.3	0.189	4334	0.986	0.075	0.203	0.945	99
1.81-1.86	7.3	0.158	4319	0.988	0.063	0.171	0.968	99.2
1.86-1.91	7.2	0.132	4338	0.991	0.053	0.142	0.992	99.3
1.91-1.97	7.2	0.112	4350	0.993	0.045	0.121	1.01	99.4
1.97-2.03	7.2	0.099	4315	0.994	0.04	0.107	1.049	99.4
2.03-2.1	7.2	0.088	4361	0.994	0.035	0.095	1.127	99.6
2.1-2.19	7.2	0.079	4344	0.995	0.032	0.086	1.147	99.7
2.19-2.28	7.3	0.074	4363	0.996	0.029	0.079	1.095	99.7
2.28-2.4	7.3	0.065	4363	0.996	0.026	0.07	0.958	99.8
2.4-2.56	7.3	0.06	4384	0.996	0.024	0.065	0.897	99.9
2.56-2.75	7.3	0.061	4383	0.996	0.024	0.065	0.988	99.9
2.75-3.03	7.1	0.059	4378	0.996	0.024	0.063	1.046	99.8
3.03-3.47	7.2	0.051	4390	0.997	0.021	0.055	0.898	99.5
3.47-4.37	6.9	0.043	4376	0.997	0.018	0.047	0.686	98.3
4.37-50	6.4	0.042	4266	0.997	0.018	0.046	0.617	93.5

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Processing

Software

Name	Version	Classification
HKL-2000		data reduction
SCALEPACK		data scaling
PHENIX	1.19.2_4158	refinement
PDB_EXTRACT	3.27	data extraction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1hqt

1hqt

Resolution: 1.61→38.79 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.1 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1789	4348	5.02 %
R_work	0.1565	82268	-
obs	0.1576	86616	98.69 %

Solvent computation

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

Displacement parameters

B_iso max: 90.2 Å² / B_iso mean: 21.0313 Å² / B_iso min: 4.3 Å²

Refinement step

Cycle: final / Resolution: 1.61→38.79 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4860	0	0	859	5719
B_iso mean	-	-	-	31.19	-
Num. residues	-	-	-	-	613

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4977
X-RAY DIFFRACTION	f_angle_d	0.877	6746
X-RAY DIFFRACTION	f_dihedral_angle_d	5.794	662
X-RAY DIFFRACTION	f_chiral_restr	0.06	784
X-RAY DIFFRACTION	f_plane_restr	0.009	844

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.61-1.63	0.2092	117	0.1831	2543	2660	92
1.63-1.65	0.1922	146	0.1796	2689	2835	98
1.65-1.67	0.1992	153	0.1766	2720	2873	98
1.67-1.69	0.1929	154	0.1769	2719	2873	99
1.69-1.71	0.2039	147	0.1731	2712	2859	99
1.71-1.74	0.203	137	0.1691	2707	2844	99
1.74-1.76	0.1917	163	0.1681	2707	2870	99
1.76-1.79	0.1603	142	0.1648	2790	2932	99
1.79-1.81	0.1948	162	0.1685	2672	2834	99
1.81-1.84	0.209	148	0.1703	2752	2900	99
1.84-1.88	0.1845	163	0.1612	2715	2878	99
1.88-1.91	0.1789	168	0.1604	2734	2902	99
1.91-1.95	0.1795	141	0.1575	2726	2867	99
1.95-1.99	0.1792	150	0.1548	2758	2908	99
1.99-2.03	0.1691	143	0.1492	2743	2886	99
2.03-2.08	0.1759	137	0.1497	2786	2923	100
2.08-2.13	0.1681	154	0.154	2736	2890	100
2.13-2.19	0.1776	162	0.1546	2763	2925	100
2.19-2.25	0.1834	134	0.1547	2768	2902	100
2.25-2.32	0.1853	143	0.1559	2785	2928	100
2.32-2.41	0.1641	137	0.1562	2760	2897	100
2.41-2.5	0.1859	132	0.1539	2825	2957	100
2.5-2.62	0.1876	128	0.1537	2764	2892	100
2.62-2.75	0.1887	145	0.162	2794	2939	100
2.75-2.93	0.2146	135	0.1601	2814	2949	100
2.93-3.15	0.182	144	0.1497	2769	2913	99
3.15-3.47	0.1654	152	0.1464	2776	2928	100
3.47-3.97	0.1625	145	0.1371	2781	2926	99
3.97-5	0.1518	140	0.1409	2745	2885	96
5-38.79	0.1785	126	0.1838	2715	2841	93

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	2.3229	0.0278	0.3267	1.7369	1.054	4.2233	0.0694	0.2744	0.0698	-0.226	-0.1284	0.1587	0.0465	-0.1979	0.0718	0.0755	0.0184	-0.0049	0.0856	0.0179	0.1287	29.6307	26.664	-10.9768
2	1.5157	0.0593	-0.141	0.9411	0.0596	1.403	0.0325	-0.0114	0.0031	-0.0886	-0.0662	-0.0664	0.0337	0.0706	0.0472	0.0525	0.007	-0.0056	0.0424	-0.0091	0.0681	36.1251	18.0542	-0.4918
3	2.1843	0.4324	0.4202	1.1779	-0.0701	1.4739	0.0939	-0.0639	0.1525	-0.0227	-0.0007	0.126	-0.1087	0.0229	-0.0013	0.0757	-0.0135	0.0138	0.0563	-0.0398	0.1327	22.0418	27.0716	5.9488
4	1.32	0.1965	-0.2283	0.89	0.9463	1.4515	0.1072	0.1265	-0.1558	-0.0333	-0.1255	0.0475	0.2139	-0.0238	-0.026	0.1434	0.0671	-0.0889	0.1518	0.0057	0.3163	5.7859	27.5564	-10.878
5	3.0313	-0.5278	-0.187	1.969	-1.3113	2.6304	0.1363	0.2845	0.2723	-0.205	-0.1359	0.1165	-0.0324	-0.0487	-0.0053	0.0936	0.0168	-0.0351	0.0892	0.0124	0.2308	15.393	33.3156	-8.5849
6	1.4472	-2.3654	0.7207	4.1179	-1.2854	0.4036	0.0744	0.0294	-0.0874	-0.2303	-0.0181	0.2999	0.1077	-0.1171	-0.0358	0.1311	-0.0216	-0.031	0.1225	-0.035	0.1653	15.9348	13.0993	4.4038
7	4.5547	-0.8106	-2.2133	2.8983	0.7669	3.8174	-0.0609	-0.0861	-0.0398	0.0519	-0.088	0.3001	-0.0178	-0.0474	0.0643	0.1402	-0.0128	-0.0064	0.2566	0.0312	0.0551	8.6537	9.4401	38.3527
8	0.5471	-0.0853	-0.5505	0.4825	0.2653	1.0796	0.005	-0.494	0.1196	0.1434	0.0691	0.0337	-0.0914	0.3864	0.045	0.1411	-0.0525	0.0009	0.3783	-0.0816	0.045	19.9892	18.8196	33.7171
9	1.9262	-1.2622	1.0357	1.1352	-1.2083	1.7949	0.0181	0.1764	-0.4106	-0.1382	-0.0883	0.2349	0.2897	-0.0164	0.0395	0.1305	-0.05	0.0043	0.108	-0.0369	0.1476	14.43	5.5299	17.515
10	1.1436	0.0236	-1.2497	0.9711	0.3883	1.5409	-0.0323	0.101	0.0738	-0.2845	0.0036	0.3217	-0.0445	-0.2611	-0.0308	0.1556	-0.0375	-0.0292	0.1685	-0.0002	0.2092	3.9317	10.2203	21.9408
11	2.1412	0.8713	0.2609	1.8062	0.1019	1.9158	-0.1238	-0.1971	-0.0791	0.1456	-0.091	0.3029	0.2368	-0.3415	0.0631	0.184	-0.069	0.0752	0.1899	-0.0305	0.2446	-0.0546	1.7307	27.981
12	1.5353	1.7745	-0.7483	3.7007	-0.6286	0.7258	-0.0974	0.0763	-0.045	0.0037	0.0831	0.1178	0.1103	-0.131	0.013	0.1647	-0.0564	0.003	0.165	-0.0482	0.2076	6.5737	9.9445	17.2948

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 37 )	A	1 - 37
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 38 through 164 )	A	38 - 164
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 165 through 219 )	A	165 - 219
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 220 through 243 )	A	220 - 243
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 244 through 291 )	A	244 - 291
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 292 through 310 )	A	292 - 310
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 1 through 37 )	B	1 - 37
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 38 through 185 )	B	38 - 185
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 186 through 202 )	B	186 - 202
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 203 through 230 )	B	203 - 230
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 231 through 277 )	B	231 - 277
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 278 through 310 )	B	278 - 310

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