PDB-9d6z: Crystal structure of Human Prostaglandin reductase 1 (PTGR1) in c...

ID or keywords:

Entry

Database: PDB / ID: 9d6z

Title

Crystal structure of Human Prostaglandin reductase 1 (PTGR1) in complex with methotrexate (Orthorhombic C form)

Components

Prostaglandin reductase 1

Keywords

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

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: 1.75 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 methotrexate (Orthorhombic C form)
Authors: Enayati, P. / Lovell, S. / 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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PDBx/mmCIF format	9d6z.cif.gz	278.7 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	9d6z_validation.pdf.gz	959.3 KB	Display	wwPDB validaton report
Full document	9d6z_full_validation.pdf.gz	960.8 KB	Display
Data in XML	9d6z_validation.xml.gz	36.7 KB	Display
Data in CIF	9d6z_validation.cif.gz	52.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/d6/9d6z ftp://data.pdbj.org/pub/pdb/validation_reports/d6/9d6z	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) #34 - Oct 2002 Dihydrofolate Reductase similarity (1) #32 - Aug 2002 Chaperones similarity (1)

Deposited unit

A: Prostaglandin reductase 1

B: Prostaglandin reductase 1

hetero molecules

77.7 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)	91.473, 98.209, 174.444
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-558- HOH
2	1	B-794- HOH

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Protein , 1 types, 2 molecules AB

#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.: 2 / 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)+]

#1: Protein

Prostaglandin reductase 1 / PRG-1 / 15-oxoprostaglandin 13-reductase / Dithiolethione-inducible gene 1 protein / D3T-inducible ...

Mass: 37959.938 Da / Num. of mol.: 2 / 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)+]

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Non-polymers , 5 types, 670 molecules

#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-DMS / DIMETHYL SULFOXIDE Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆OS / Comment: DMSO, precipitant*YM
#4: Chemical	ChemComp-MTX / METHOTREXATE Mass: 454.439 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₀H₂₂N₈O₅ / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 651 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.58 Å³/Da / Density % sol: 52.33 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Berkeley B2: 30% (w/v) PEG 3350, 100 mM Hepes free acid/ Sodium hydroxide pH 7.5, 400 mM Sodium chloride. HosaA.00871.a.A2.PW39298 at 16.1 mg/mL. His tag removed with 3C protease. 20 hour ...Details: Berkeley B2: 30% (w/v) PEG 3350, 100 mM Hepes free acid/ Sodium hydroxide pH 7.5, 400 mM Sodium chloride. HosaA.00871.a.A2.PW39298 at 16.1 mg/mL. His tag removed with 3C protease. 20 hour soak in 5mM methotrexate in crystallant. Plate01-Clover A2, Puck: PSL0602, Cryo: Direct.

Crystal

Density Matthews: 2.58 Å³/Da / Density % sol: 52.33 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Berkeley B2: 30% (w/v) PEG 3350, 100 mM Hepes free acid/ Sodium hydroxide pH 7.5, 400 mM Sodium chloride. HosaA.00871.a.A2.PW39298 at 16.1 mg/mL. His tag removed with 3C protease. 20 hour ...

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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: 1.75→49.1 Å / Num. obs: 79264 / % possible obs: 100 % / Redundancy: 13.1 % / CC_1/2: 0.996 / R_merge(I) obs: 0.174 / R_pim(I) all: 0.05 / R_rim(I) all: 0.181 / Χ²: 1.03 / Net I/σ(I): 9.9 / Num. measured all: 1039140
Reflection shell	Resolution: 1.75→1.78 Å / % possible obs: 100 % / Redundancy: 13 % / R_merge(I) obs: 1.574 / Num. measured all: 55882 / Num. unique obs: 4303 / CC_1/2: 0.658 / R_pim(I) all: 0.451 / R_rim(I) all: 1.639 / Χ²: 0.94 / Net I/σ(I) obs: 1.8

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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: 1.75→47.27 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.01 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1935	4027	5.09 %
R_work	0.1662	-	-
obs	0.1676	79192	99.94 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.75→47.27 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5020	0	107	651	5778

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	5258
X-RAY DIFFRACTION	f_angle_d	0.926	7117
X-RAY DIFFRACTION	f_dihedral_angle_d	13.353	1995
X-RAY DIFFRACTION	f_chiral_restr	0.054	795
X-RAY DIFFRACTION	f_plane_restr	0.008	918

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 (%)
1.75-1.77	0.3795	132	0.335	2596	X-RAY DIFFRACTION	100
1.77-1.79	0.3604	152	0.3216	2516	X-RAY DIFFRACTION	100
1.79-1.81	0.3091	149	0.2857	2594	X-RAY DIFFRACTION	100
1.81-1.84	0.2952	126	0.2657	2537	X-RAY DIFFRACTION	100
1.84-1.86	0.2586	128	0.2235	2638	X-RAY DIFFRACTION	100
1.86-1.89	0.2316	140	0.2107	2526	X-RAY DIFFRACTION	100
1.89-1.92	0.2107	118	0.1907	2608	X-RAY DIFFRACTION	100
1.92-1.95	0.2316	123	0.1685	2564	X-RAY DIFFRACTION	100
1.95-1.98	0.2274	149	0.1649	2577	X-RAY DIFFRACTION	100
1.98-2.01	0.2022	165	0.1619	2512	X-RAY DIFFRACTION	100
2.01-2.05	0.2201	161	0.1576	2568	X-RAY DIFFRACTION	100
2.05-2.09	0.2075	127	0.1638	2571	X-RAY DIFFRACTION	100
2.09-2.13	0.1983	138	0.1745	2581	X-RAY DIFFRACTION	100
2.13-2.18	0.2024	142	0.1792	2594	X-RAY DIFFRACTION	100
2.18-2.23	0.233	144	0.1828	2576	X-RAY DIFFRACTION	100
2.23-2.29	0.184	146	0.1723	2547	X-RAY DIFFRACTION	100
2.29-2.35	0.1912	150	0.1476	2557	X-RAY DIFFRACTION	100
2.35-2.42	0.1798	144	0.1466	2591	X-RAY DIFFRACTION	100
2.42-2.5	0.1981	160	0.1424	2577	X-RAY DIFFRACTION	100
2.5-2.58	0.1717	132	0.1481	2604	X-RAY DIFFRACTION	100
2.58-2.69	0.1756	117	0.1497	2614	X-RAY DIFFRACTION	100
2.69-2.81	0.2049	119	0.1578	2607	X-RAY DIFFRACTION	100
2.81-2.96	0.1867	125	0.1639	2601	X-RAY DIFFRACTION	100
2.96-3.14	0.1715	143	0.1682	2589	X-RAY DIFFRACTION	100
3.14-3.39	0.1737	139	0.1572	2634	X-RAY DIFFRACTION	100
3.39-3.73	0.1679	147	0.1502	2618	X-RAY DIFFRACTION	100
3.73-4.27	0.1478	127	0.1377	2630	X-RAY DIFFRACTION	100
4.27-5.37	0.1528	140	0.1352	2660	X-RAY DIFFRACTION	100
5.37-47.27	0.2166	144	0.1928	2778	X-RAY DIFFRACTION	100

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	1.0594	0.4774	-1.4223	0.8047	-0.7964	4.416	-0.0414	-0.0257	-0.0925	-0.0328	0.067	-0.0402	0.3619	-0.0165	-0.0048	0.1333	0.0002	-0.0301	0.1195	-0.0008	0.133	15.2445	-1.9092	-21.2353
2	2.6318	3.0997	2.514	4.2493	4.4166	5.9425	0.1607	-0.2302	-0.2372	0.329	0.2313	-0.3715	0.2292	0.1593	-0.3354	0.2337	0.0173	0.0396	0.3065	0.0189	0.2107	16.5406	2.3422	-6.445
3	4.844	2.5537	-1.5442	3.2731	-0.57	1.9512	0.0866	-0.1263	0.1055	0.1584	-0.0632	-0.0301	-0.0233	-0.0059	-0.0168	0.1406	0.0185	-0.0093	0.0889	-0.0086	0.0964	32.3688	17.0659	-12.7973
4	3.304	-0.069	2.2831	2.5531	0.0036	7.6479	-0.0305	-0.082	0.1295	0.1129	0.2137	0.2613	-0.3171	-0.5342	-0.1801	0.1574	0.0081	0.0297	0.1114	0.0545	0.1946	30.2401	27.2914	-18.8683
5	2.66	-0.179	0.4248	3.242	-0.0645	2.2768	-0.0515	0.165	0.217	-0.0754	-0.0048	-0.144	-0.1238	0.0401	0.0462	0.1276	-0.005	0.0085	0.0863	0.0167	0.1231	41.2137	22.6575	-24.8899
6	1.2993	0.022	0.4256	0.3937	-0.0025	0.5411	-0.0242	-0.0212	-0.0194	0.0672	-0.0049	-0.0106	0.0233	-0.0499	0.0287	0.1937	-0.0043	0.0108	0.1346	-0.0014	0.1668	29.6752	12.3053	-19.4851
7	1.2934	0.3832	0.6646	1.0727	0.2225	1.9226	-0.0434	-0.0614	0.0649	0.0505	0.0051	-0.091	-0.2833	0.0859	0.051	0.1359	-0.0113	0.0116	0.1238	0.0066	0.1517	80.7136	17.1319	-29.6429
8	1.5455	0.0735	-0.4283	0.4906	0.003	0.4658	0.0045	-0.0114	-0.0997	0.0284	-0.0243	-0.0062	0.0417	0.0227	-0.0083	0.151	0.0002	-0.0132	0.1165	0.0152	0.1563	62.5856	-0.4594	-25.328

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 93 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 94 through 112 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 113 through 164 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 165 through 185 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 186 through 243 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 244 through 329 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 2 through 112 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 113 through 329 )

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