PDB-9mde: Crystal structure of Human Prostaglandin reductase 1 (PTGR1) in c...

ID or keywords:

Entry

Database: PDB / ID: 9mde

Title

Crystal structure of Human Prostaglandin reductase 1 (PTGR1) in complex with NADP

Components

Prostaglandin reductase 1

Keywords

OXIDOREDUCTASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Prostaglandin reductase 1 / indomethacin

Function / homology

Function and homology information

leukotriene B4 metabolic process / 13-lipoxin reductase activity / leukotriene B4 12-hydroxy dehydrogenase activity / lipoxin A4 metabolic process / 2-alkenal reductase [NAD(P)+] / 2-alkenal reductase (NADPH) activity / 13,14-dehydro-15-oxoprostaglandin 13-reductase / 15-oxoprostaglandin 13-reductase [NAD(P)+] activity / Biosynthesis of Lipoxins (LX) / leukotriene metabolic process ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	75N93022C00036	United States
National Institutes of Health/Office of the Director	S10OD030394	United States

Citation

Journal: To be published
Title: Crystal structure of Human Prostaglandin reductase 1 (PTGR1) in complex with NADP
Authors: Lovell, S. / Cooper, A. / Battaile, K.P.

History

Deposition	Dec 5, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 10, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9mde.cif.gz	512.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9mde.ent.gz	421.9 KB	Display	PDB format
PDBx/mmJSON format	9mde.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9mde_validation.pdf.gz	2.5 MB	Display	wwPDB validaton report
Full document	9mde_full_validation.pdf.gz	2.5 MB	Display
Data in XML	9mde_validation.xml.gz	60.9 KB	Display
Data in CIF	9mde_validation.cif.gz	78.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/md/9mde ftp://data.pdbj.org/pub/pdb/validation_reports/md/9mde	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	#13 - Jan 2001 Alcohol Dehydrogenase similarity (5) #222 - Jun 2018 Proteins and Nanoparticles similarity (1) #32 - Aug 2002 Chaperones similarity (1)

Deposited unit

A: Prostaglandin reductase 1

B: Prostaglandin reductase 1

C: Prostaglandin reductase 1

D: Prostaglandin reductase 1

hetero molecules

148 kDa, 4 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)	67.195, 68.048, 84.274
Angle α, β, γ (deg.)	69.81, 86.75, 85.57
Int Tables number	1
Space group name H-M	P1

#1: Protein	Prostaglandin reductase 1 / PRG-1 / 15-oxoprostaglandin 13-reductase / Dithiolethione-inducible gene 1 protein / D3T-inducible ...PRG-1 / 15-oxoprostaglandin 13-reductase / Dithiolethione-inducible gene 1 protein / D3T-inducible gene 1 protein / DIG-1 / Leukotriene B4 12-hydroxydehydrogenase / NAD(P)H-dependent alkenal/one oxidoreductase Mass: 35968.734 Da / Num. of mol.: 4 / Fragment: T4-A329 / Mutation: A27S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTGR1, LTB4DH / Plasmid: HosaA.00871.a.A2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q14914, 13,14-dehydro-15-oxoprostaglandin 13-reductase, 2-alkenal reductase [NAD(P)+]
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₈N₇O₁₇P₃ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE Mass: 266.331 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₂H₂₆O₆
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 552 / 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: 2.5 Å³/Da / Density % sol: 50.9 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Berkeley B2: 30% (w/v) PEG 3350, 100 mM Hepes pH 7.5, 400 mM sodium chloride. HosaA.00871.a.A2.PW39298 at 16.1 mg/mL. His tag cleaved with 3C protease. 2mM NADP+ added prior to ...Details: Berkeley B2: 30% (w/v) PEG 3350, 100 mM Hepes pH 7.5, 400 mM sodium chloride. HosaA.00871.a.A2.PW39298 at 16.1 mg/mL. His tag cleaved with 3C protease. 2mM NADP+ added prior to crystallization, plate 14493 well B2 drop 1 , Puck: PSL1909, Cryo: 50% crystallant + 50% PEG 3350 (37.5% PEG 3350 total).

Crystal

Density Matthews: 2.5 Å³/Da / Density % sol: 50.9 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Berkeley B2: 30% (w/v) PEG 3350, 100 mM Hepes pH 7.5, 400 mM sodium chloride. HosaA.00871.a.A2.PW39298 at 16.1 mg/mL. His tag cleaved with 3C protease. 2mM NADP+ added prior to ...

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Oct 24, 2024
Radiation	Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9786 Å / Relative weight: 1
Reflection	Resolution: 2→47.66 Å / Num. obs: 91664 / % possible obs: 97.2 % / Redundancy: 3.5 % / CC_1/2: 0.981 / R_merge(I) obs: 0.111 / R_pim(I) all: 0.071 / R_rim(I) all: 0.133 / Χ²: 0.4 / Net I/σ(I): 6.2 / Num. measured all: 318724
Reflection shell	Resolution: 2→2.03 Å / % possible obs: 96.9 % / Redundancy: 3.6 % / R_merge(I) obs: 0.68 / Num. measured all: 16144 / Num. unique obs: 4522 / CC_1/2: 0.659 / R_pim(I) all: 0.422 / R_rim(I) all: 0.803 / Χ²: 0.37 / Net I/σ(I) obs: 1.8

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Processing

Software

Name	Version	Classification
PHENIX	dev_5493	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2→47.66 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 19.31 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2093	4486	4.89 %
R_work	0.1674	-	-
obs	0.1694	91654	97.16 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2→47.66 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9940	0	249	552	10741

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	10404
X-RAY DIFFRACTION	f_angle_d	0.571	14104
X-RAY DIFFRACTION	f_dihedral_angle_d	14.551	4040
X-RAY DIFFRACTION	f_chiral_restr	0.043	1596
X-RAY DIFFRACTION	f_plane_restr	0.004	1746

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 (%)
2-2.02	0.2486	154	0.2164	2877	X-RAY DIFFRACTION	97
2.02-2.05	0.2729	143	0.214	2925	X-RAY DIFFRACTION	97
2.05-2.07	0.2622	159	0.2135	2833	X-RAY DIFFRACTION	97
2.07-2.1	0.2361	172	0.2107	2933	X-RAY DIFFRACTION	97
2.1-2.13	0.2272	171	0.2039	2844	X-RAY DIFFRACTION	97
2.13-2.15	0.2347	169	0.1974	2914	X-RAY DIFFRACTION	97
2.15-2.19	0.2408	169	0.1932	2853	X-RAY DIFFRACTION	97
2.19-2.22	0.2585	162	0.1929	2924	X-RAY DIFFRACTION	98
2.22-2.25	0.2543	150	0.1898	2905	X-RAY DIFFRACTION	97
2.25-2.29	0.2457	175	0.2014	2869	X-RAY DIFFRACTION	97
2.29-2.33	0.262	143	0.186	2938	X-RAY DIFFRACTION	97
2.33-2.37	0.2227	153	0.1788	2848	X-RAY DIFFRACTION	96
2.37-2.42	0.2051	145	0.1779	2914	X-RAY DIFFRACTION	97
2.42-2.47	0.2586	136	0.1704	2944	X-RAY DIFFRACTION	98
2.47-2.52	0.2135	130	0.1671	2923	X-RAY DIFFRACTION	98
2.52-2.58	0.213	133	0.1704	2949	X-RAY DIFFRACTION	98
2.58-2.64	0.2386	155	0.1749	2894	X-RAY DIFFRACTION	98
2.64-2.71	0.1788	135	0.171	2992	X-RAY DIFFRACTION	98
2.71-2.79	0.2621	149	0.1748	2898	X-RAY DIFFRACTION	98
2.79-2.88	0.2167	146	0.1748	2908	X-RAY DIFFRACTION	98
2.88-2.99	0.2489	166	0.18	2966	X-RAY DIFFRACTION	98
2.99-3.11	0.1868	148	0.1777	2904	X-RAY DIFFRACTION	98
3.11-3.25	0.2065	147	0.1768	2958	X-RAY DIFFRACTION	98
3.25-3.42	0.2454	149	0.1815	2896	X-RAY DIFFRACTION	97
3.42-3.63	0.1735	166	0.1575	2876	X-RAY DIFFRACTION	97
3.63-3.91	0.1926	167	0.1492	2878	X-RAY DIFFRACTION	97
3.91-4.31	0.1519	113	0.1317	2936	X-RAY DIFFRACTION	97
4.31-4.93	0.1422	112	0.1212	2866	X-RAY DIFFRACTION	95
4.93-6.21	0.1828	136	0.1478	2917	X-RAY DIFFRACTION	97
6.21-47.66	0.1937	133	0.1587	2886	X-RAY DIFFRACTION	96

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	1.2034	-0.067	-0.5219	0.9834	-0.0287	1.897	0.0035	0.0919	0.066	0.02	0.0576	0.1209	0.1079	-0.4365	-0.0465	0.153	-0.0275	-0.0151	0.2552	0.0306	0.1882	-9.2176	-20.9342	-5.9468
2	1.5989	-0.7356	-0.0436	1.4992	-0.1398	0.9666	0.0354	0.0113	0.0338	-0.0783	-0.0467	-0.104	0.033	0.06	0.0141	0.1469	-0.0151	-0.0058	0.1406	-0.0005	0.1677	19.8843	-25.7958	-2.2476
3	0.6405	-0.3935	0.1831	0.5732	-0.1217	1.784	0.0205	0.0425	0.1077	-0.0105	0.051	-0.0002	-0.1491	-0.0345	-0.0695	0.1505	-0.016	0.0077	0.1583	0.0069	0.2066	4.9635	-15.4048	-0.9645
4	0.8362	0.44	-0.0631	1.9989	0.1574	1.6136	-0.0151	-0.044	0.066	-0.0556	0.008	0.1412	-0.3121	0.074	0.0152	0.2392	-0.0126	-0.0167	0.1402	-0.0111	0.1661	7.7986	-3.5629	-40.3221
5	1.2613	-0.3675	0.0676	1.8242	-0.1313	1.2039	-0.0201	0.001	-0.0887	-0.0073	0.0075	0.0327	0.0406	0.0605	0.0116	0.1632	-0.031	-0.0031	0.1663	-0.0173	0.1562	8.9986	-32.3479	-46.5892
6	0.5271	0.1081	0.3277	1.2346	1.1801	2.3262	-0.0304	0.0224	0.0814	-0.0412	-0.1432	0.166	-0.0826	-0.0739	0.1456	0.2073	-0.0003	-0.0211	0.1777	0.0136	0.2505	0.6066	-18.1019	-47.2577
7	1.437	-0.3457	0.6919	1.0609	-0.2202	1.5615	-0.1314	-0.0022	-0.0818	0.1251	0.1414	-0.0259	-0.1244	0.121	-0.0027	0.2266	0.049	0.0174	0.2697	0.0287	0.239	49.2723	-58.1948	-2.0009
8	1.5784	0.1706	0.287	1.2173	-0.2473	1.3046	-0.0213	-0.0796	-0.3044	0.0395	-0.0352	0.2528	0.1646	-0.0583	0.0713	0.2294	0.0106	0.0429	0.1677	0.0303	0.3179	21.4581	-61.3622	-1.1912
9	1.3022	-0.1465	-0.5805	1.1666	0.1294	1.2442	0.0324	0.0935	-0.0913	-0.0227	-0.0489	0.3005	-0.0821	-0.144	0.0414	0.214	0.0099	0.0045	0.1898	0.0041	0.2985	14.8412	-51.0513	-7.0224
10	1.516	-0.7694	-0.4961	1.0738	0.5832	0.4173	-0.0298	-0.0779	-0.2074	0.0868	-0.0106	0.1186	0.0297	0.1189	0.0043	0.2237	-0.0085	0.0181	0.2081	0.0426	0.2618	29.5001	-56.6054	-2.2524
11	1.0442	0.1892	0.395	0.7943	0.1069	1.4658	0.1906	0.1507	-0.3585	-0.2402	0.0266	0.0735	0.6452	-0.1483	-0.1513	0.5061	0.0161	-0.0949	0.2955	-0.0357	0.3527	38.0258	-66.0385	-39.8464
12	1.6	-0.5728	0.5225	1.5201	-0.1687	0.908	0.0525	0.0741	0.0977	-0.0521	-0.0741	-0.0838	0.0676	0.0964	0.027	0.1593	-0.0027	0.0291	0.2248	0.0237	0.178	38.6669	-39.1227	-43.2293
13	0.906	0.1843	-0.1168	1.0339	-0.2178	1.7101	0.1674	0.1352	-0.0924	-0.0932	-0.1251	-0.3147	0.215	0.182	-0.009	0.2848	0.0926	0.0264	0.3336	0.0153	0.3058	46.6893	-52.0113	-44.3917

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 112 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 113 through 276 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 277 through 329 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 1 through 102 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 103 through 277 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 278 through 329 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 2 through 112 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 113 through 198 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 199 through 245 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 246 through 329 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 2 through 93 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 94 through 276 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 277 through 329 )

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