PDB-9d6w: Crystal structure of Apo Human Prostaglandin reductase 1 (PTGR1) ...

ID or keywords:

Entry

Database: PDB / ID: 9d6w

Title

Crystal structure of Apo Human Prostaglandin reductase 1 (PTGR1) (Monoclinic P form)

Components

Prostaglandin reductase 1

Keywords

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

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: 2.1 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 Apo Human Prostaglandin reductase 1 (PTGR1) (Monoclinic P form)
Authors: Lovell, S. / Enayati, P. / Cooper, A. / Liu, L. / Battaile, K.P.

History

Deposition	Aug 16, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 20, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9d6w.cif.gz	511 KB	Display	PDBx/mmCIF format
PDB format	pdb9d6w.ent.gz	421.3 KB	Display	PDB format
PDBx/mmJSON format	9d6w.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9d6w_validation.pdf.gz	463.3 KB	Display	wwPDB validaton report
Full document	9d6w_full_validation.pdf.gz	465.6 KB	Display
Data in XML	9d6w_validation.xml.gz	53 KB	Display
Data in CIF	9d6w_validation.cif.gz	69.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/d6/9d6w ftp://data.pdbj.org/pub/pdb/validation_reports/d6/9d6w	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) #32 - Aug 2002 Chaperones similarity (1) #70 - Oct 2005 Designer Proteins similarity (1)

Deposited unit

A: Prostaglandin reductase 1

B: Prostaglandin reductase 1

C: Prostaglandin reductase 1

D: Prostaglandin reductase 1

hetero molecules

152 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Prostaglandin reductase 1

D: Prostaglandin reductase 1

hetero molecules

defined by author&software
Evidence: gel filtration
76 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Prostaglandin reductase 1

C: Prostaglandin reductase 1

hetero molecules

defined by author&software
76.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	91.472, 82.869, 98.512
Angle α, β, γ (deg.)	90.00, 90.04, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#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: 37959.938 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.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O / Comment: alkaloid*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
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: 2.46 Å³/Da / Density % sol: 49.98 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Index D11: 28% w/v Polyethylene glycol monomethyl ether 2,000, 0.1 M BIS-TRIS pH 6.5. HosaA.00871.a.A2.PW39293 at 24.7 mg/mL. plate 14261 well D11 Drop 1, Puck: PSL0106, Cryo: 80% crystallant + 20% PEG 200.

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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: Aug 4, 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: 2.1→49.26 Å / Num. obs: 85808 / % possible obs: 99.7 % / Redundancy: 6.8 % / CC_1/2: 0.996 / R_merge(I) obs: 0.099 / R_pim(I) all: 0.042 / R_rim(I) all: 0.108 / Χ²: 1.07 / Net I/σ(I): 10.8 / Num. measured all: 584079
Reflection shell	Resolution: 2.1→2.14 Å / % possible obs: 100 % / Redundancy: 6.4 % / R_merge(I) obs: 0.838 / Num. measured all: 29289 / Num. unique obs: 4559 / CC_1/2: 0.816 / R_pim(I) all: 0.358 / R_rim(I) all: 0.913 / Χ²: 1 / Net I/σ(I) obs: 2.2

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Processing

Software

Name	Version	Classification
PHENIX	dev_5421	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.1→49.26 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.27 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2393	4165	4.86 %
R_work	0.2087	-	-
obs	0.2102	85775	99.68 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.1→49.26 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9931	0	19	298	10248

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	10157
X-RAY DIFFRACTION	f_angle_d	0.628	13750
X-RAY DIFFRACTION	f_dihedral_angle_d	12.213	3741
X-RAY DIFFRACTION	f_chiral_restr	0.046	1562
X-RAY DIFFRACTION	f_plane_restr	0.006	1736

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 (%)
2.1-2.12	0.346	120	0.3014	2708	X-RAY DIFFRACTION	100
2.12-2.15	0.319	164	0.2661	2676	X-RAY DIFFRACTION	100
2.15-2.18	0.2832	140	0.2344	2773	X-RAY DIFFRACTION	100
2.18-2.2	0.2453	124	0.2278	2694	X-RAY DIFFRACTION	100
2.2-2.23	0.2856	122	0.2177	2743	X-RAY DIFFRACTION	100
2.23-2.26	0.2279	124	0.2268	2708	X-RAY DIFFRACTION	100
2.26-2.29	0.2959	134	0.2227	2759	X-RAY DIFFRACTION	100
2.29-2.33	0.2785	168	0.2194	2643	X-RAY DIFFRACTION	100
2.33-2.37	0.2782	140	0.2122	2760	X-RAY DIFFRACTION	100
2.37-2.4	0.2848	129	0.209	2685	X-RAY DIFFRACTION	100
2.4-2.45	0.2967	133	0.204	2734	X-RAY DIFFRACTION	100
2.45-2.49	0.2392	133	0.2083	2697	X-RAY DIFFRACTION	100
2.49-2.54	0.2372	163	0.2138	2730	X-RAY DIFFRACTION	100
2.54-2.59	0.2863	124	0.216	2740	X-RAY DIFFRACTION	100
2.59-2.65	0.2832	134	0.2277	2676	X-RAY DIFFRACTION	100
2.65-2.71	0.275	137	0.241	2724	X-RAY DIFFRACTION	100
2.71-2.78	0.2919	110	0.2483	2768	X-RAY DIFFRACTION	100
2.78-2.85	0.2767	134	0.2422	2738	X-RAY DIFFRACTION	100
2.85-2.93	0.3053	125	0.225	2730	X-RAY DIFFRACTION	100
2.93-3.03	0.2356	137	0.2203	2715	X-RAY DIFFRACTION	100
3.03-3.14	0.2706	167	0.2226	2695	X-RAY DIFFRACTION	100
3.14-3.26	0.2423	148	0.2239	2698	X-RAY DIFFRACTION	100
3.26-3.41	0.2661	138	0.2281	2741	X-RAY DIFFRACTION	100
3.41-3.59	0.2185	157	0.2102	2679	X-RAY DIFFRACTION	99
3.59-3.82	0.225	165	0.1943	2675	X-RAY DIFFRACTION	98
3.82-4.11	0.1984	156	0.1803	2675	X-RAY DIFFRACTION	98
4.11-4.52	0.2146	146	0.1775	2704	X-RAY DIFFRACTION	99
4.52-5.18	0.202	145	0.1783	2755	X-RAY DIFFRACTION	100
5.18-6.52	0.2095	123	0.2096	2765	X-RAY DIFFRACTION	99
6.52-49.26	0.2192	125	0.2044	2822	X-RAY DIFFRACTION	99

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	3.411	-1.0368	0.0468	2.3083	0.8051	1.4691	-0.0167	-0.5942	0.246	0.3031	0.0253	-0.4795	0.1476	-0.1786	-0.0302	0.4348	0.0166	0.026	0.4757	0.1365	0.3886	-34.7003	-45.4137	-8.7202
2	1.3219	0.9995	-0.7349	5.8403	1.0979	1.8571	0.0442	-0.0556	0.1199	-0.0801	0.1011	-0.7276	-0.0203	0.2913	-0.1314	0.2408	-0.026	-0.0262	0.3585	0.0898	0.5325	-20.3067	-34.6174	-21.4141
3	3.4949	0.8415	0.4991	3.215	-1.0985	3.4009	-0.0538	0.4221	-0.408	-0.4388	0.1705	0.4323	0.4282	-0.4499	-0.1457	0.401	-0.0306	-0.0849	0.6519	-0.027	0.5106	-84.6601	-38.355	-20.4578
4	3.6524	-0.1915	-0.6147	1.032	0.0246	1.6602	0.0368	0.0196	0.1546	0.0016	0.0308	0.0636	-0.1162	-0.1198	-0.0647	0.27	-0.0024	0.0097	0.3793	0.0051	0.2175	-65.3406	-29.4049	-5.5337
5	2.3702	1.0415	-0.3394	2.2767	0.8659	0.8816	0.0068	-0.5137	0.1197	0.7883	0.0798	0.6437	-0.5229	-0.9828	0.0222	0.6042	0.2298	0.1355	0.958	0.0145	0.5615	-81.1989	2.8158	-28.8169
6	1.5785	-1.2233	-0.7257	3.2492	1.0087	3.1113	-0.0898	0.2075	-0.1108	-0.0661	0.0191	0.2197	-0.032	-0.1746	0.0409	0.2674	-0.0093	-0.0301	0.4661	0.0124	0.2925	-66.0273	-3.3046	-48.5752
7	3.3622	1.1617	1.2969	2.5617	0.3066	2.2572	0.0274	0.038	-0.3681	0.085	0.0967	-0.1029	0.0252	-0.0301	-0.1364	0.3086	0.0192	-0.0185	0.3563	0.0031	0.289	-54.7127	-11.3209	-44.2408
8	3.1067	0.0108	1.4377	2.4685	-0.0069	1.348	0.1532	-0.1847	-0.4869	-0.0144	-0.0617	0.1818	0.0115	-0.2243	0.0406	0.3559	-0.063	-0.0428	0.445	0.0555	0.2742	-52.076	-2.5094	-35.9027
9	2.7575	0.6318	-0.2006	2.524	-1.5848	4.9504	-0.3267	-0.2916	-0.1221	0.0484	0.0838	0.3245	0.0681	-0.9808	0.173	0.3594	0.0672	-0.0148	0.6476	0.0341	0.4084	-76.5566	-2.116	-42.6991
10	3.0875	-0.2076	-0.3538	2.9354	-0.011	1.506	-0.1863	0.5251	0.047	-0.8328	0.0801	-0.502	0.0509	0.1743	0.1289	0.4873	-0.0431	0.1134	0.4705	0.0373	0.476	-15.1398	-5.7039	-42.9103
11	3.303	-0.6626	-1.4975	2.079	0.2909	2.1194	-0.1671	-0.0257	0.2891	0.0479	0.0435	-0.1261	-0.0107	0.022	0.1394	0.3031	-0.0207	-0.0653	0.2848	-0.0115	0.3194	-31.1367	10.1701	-28.4607
12	3.8348	-0.3704	1.2854	1.9129	0.3379	1.6304	0.0165	-0.2418	0.0405	0.0681	-0.0717	0.0938	-0.1031	-0.1351	0.0481	0.3153	-0.0327	-0.0353	0.34	0.01	0.2526	-43.3469	2.0428	-26.7796
13	2.5739	-0.4384	1.5322	3.5256	0.1017	1.2716	-0.0458	0.3101	0.1263	-0.097	-0.1008	-0.3326	-0.085	0.1359	0.176	0.3088	-0.0105	0.0787	0.3724	0.074	0.4465	-20.3855	4.8361	-31.8875
14	2.4479	0.7324	0.4471	3.673	-0.2175	4.1001	0.0665	-0.2796	0.3082	0.8246	0.1395	-0.2734	-0.2759	0.2248	-0.1312	0.4129	0.0302	-0.0437	0.3969	-0.0325	0.4595	-19.6934	-23.066	-9.2442
15	3.3813	-0.176	0.77	0.2767	-0.6922	1.7795	0.0616	-0.9349	-0.2453	1.1688	0.0383	-0.7513	0.3081	0.4955	0.0909	0.7909	0.1333	-0.3822	0.7563	0.0539	0.6455	-11.6325	-35.53	-2.0988
16	2.4716	1.2122	-0.276	5.8769	1.8818	3.8108	-0.0987	-0.7353	-0.3698	1.4515	0.1797	-0.3134	0.7401	0.7654	-0.157	0.7448	0.065	-0.1861	0.6503	0.1157	0.5591	-16.256	-41.6052	-3.5801
17	4.0994	0.1725	0.3748	1.9139	0.2453	2.1265	-0.0855	-0.1885	-0.3196	0.0721	-0.0297	-0.1872	0.0002	-0.242	0.0997	0.338	0.0391	0.0523	0.345	0.0782	0.3543	-33.4934	-45.2675	-16.9255
18	4.0427	-0.0973	-0.4944	1.4442	-0.083	2.3981	0.0774	0.5121	-0.2664	0.0176	-0.0975	-0.0623	-0.0374	-0.2169	0.0641	0.3288	0.034	0.0242	0.4035	-0.0355	0.3159	-39.6816	-41.6273	-30.2299
19	4.7237	1.5449	-0.061	2.401	0.493	1.1106	0.0983	0.1581	0.0468	0.0269	-0.1514	0.1043	0.0649	-0.1263	0.0351	0.3971	0.0658	0.0589	0.4738	0.0162	0.3027	-46.642	-36.0943	-21.2901
20	2.4546	-0.4501	-0.9002	0.8234	-0.5013	1.3929	0.3912	0.5914	0.4341	-0.2032	-0.3456	0.0954	0.1817	-0.0402	-0.0572	0.3723	0.0459	0.1187	0.4981	0.0815	0.374	-51.532	-28.6754	-21.3607

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 264 through 292 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 293 through 329 )
3	X-RAY DIFFRACTION	3	chain 'C' and (resid 2 through 112 )
4	X-RAY DIFFRACTION	4	chain 'C' and (resid 113 through 329 )
5	X-RAY DIFFRACTION	5	chain 'D' and (resid 3 through 111 )
6	X-RAY DIFFRACTION	6	chain 'D' and (resid 112 through 185 )
7	X-RAY DIFFRACTION	7	chain 'D' and (resid 186 through 245 )
8	X-RAY DIFFRACTION	8	chain 'D' and (resid 246 through 276 )
9	X-RAY DIFFRACTION	9	chain 'D' and (resid 277 through 329 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 2 through 112 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 113 through 185 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 186 through 276 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 277 through 329 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 2 through 66 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 67 through 93 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 94 through 112 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 113 through 164 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 165 through 219 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 220 through 245 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 246 through 263 )

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