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- PDB-9d71: Crystal structure of Human Prostaglandin reductase 1 (PTGR1) in c... -

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Basic information

Entry
Database: PDB / ID: 9d71
TitleCrystal structure of Human Prostaglandin reductase 1 (PTGR1) in complex with methotrexate (P1 form)
ComponentsProstaglandin reductase 1
KeywordsOXIDOREDUCTASE / 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 ...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 / Synthesis of Leukotrienes (LT) and Eoxins (EX) / prostaglandin metabolic process / extracellular exosome / cytoplasm
Similarity search - Function
Leukotriene B4 12-hydroxydehydrogenase/15-oxo-prostaglandin 13-reductase / Oxidoreductase, N-terminal domain / Medium-chain dehydrogenase/reductase / N-terminal domain of oxidoreductase / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
METHOTREXATE / Prostaglandin reductase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal structure of Human Prostaglandin reductase 1 (PTGR1) in complex with methotrexate (P1 form)
Authors: Lovell, S. / Enayati, P. / Cooper, A. / Liu, L. / Battaile, K.P.
History
DepositionAug 16, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Prostaglandin reductase 1
B: Prostaglandin reductase 1
C: Prostaglandin reductase 1
D: Prostaglandin reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,2387
Polymers143,8754
Non-polymers1,3633
Water6,431357
1
A: Prostaglandin reductase 1
C: Prostaglandin reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8464
Polymers71,9372
Non-polymers9092
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-22 kcal/mol
Surface area26840 Å2
MethodPISA
2
B: Prostaglandin reductase 1
D: Prostaglandin reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3923
Polymers71,9372
Non-polymers4541
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-20 kcal/mol
Surface area27200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.356, 67.806, 84.762
Angle α, β, γ (deg.)70.62, 87.04, 84.65
Int Tables number1
Space group name H-MP1

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Components

#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-MTX / METHOTREXATE


Mass: 454.439 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H22N8O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: chemotherapy*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Morpheus A1: 20%(v/v) PEG 500 MME, 10%(w/v) PEG 20000, 100 mM Imidazole/MES, pH 6.5, 30 mM MgCl2 and 30 mM CaCl2. HosaA.00871.a.A2.PW39298 at 16.1 mg/mL. His tag removed with 3C protease. ...Details: Morpheus A1: 20%(v/v) PEG 500 MME, 10%(w/v) PEG 20000, 100 mM Imidazole/MES, pH 6.5, 30 mM MgCl2 and 30 mM CaCl2. HosaA.00871.a.A2.PW39298 at 16.1 mg/mL. His tag removed with 3C protease. 2mM methotrexate added to the protein prior to crystallization. Plate 14264 well A1 drop 2, Puck: PSL0116, Cryo: Direct.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Aug 4, 2024
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2→48.19 Å / Num. obs: 87261 / % possible obs: 91.7 % / Redundancy: 3.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.028 / Rrim(I) all: 0.054 / Χ2: 0.79 / Net I/σ(I): 12.7 / Num. measured all: 309181
Reflection shellResolution: 2→2.04 Å / % possible obs: 96.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.628 / Num. measured all: 17196 / Num. unique obs: 4722 / CC1/2: 0.793 / Rpim(I) all: 0.383 / Rrim(I) all: 0.738 / Χ2: 0.64 / Net I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
PHENIXdev_5421refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→48.19 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 31.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.252 4385 5.03 %
Rwork0.2124 --
obs0.2144 87233 91.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→48.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10004 0 99 357 10460
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310317
X-RAY DIFFRACTIONf_angle_d0.54513971
X-RAY DIFFRACTIONf_dihedral_angle_d14.1863853
X-RAY DIFFRACTIONf_chiral_restr0.0431571
X-RAY DIFFRACTIONf_plane_restr0.0041799
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.37871600.32862923X-RAY DIFFRACTION97
2.02-2.050.32721740.3092908X-RAY DIFFRACTION97
2.05-2.060.3376650.3171437X-RAY DIFFRACTION88
2.07-2.10.33291480.30652451X-RAY DIFFRACTION94
2.1-2.130.31931520.29052940X-RAY DIFFRACTION97
2.13-2.150.36691610.29142869X-RAY DIFFRACTION97
2.15-2.190.32661390.28382978X-RAY DIFFRACTION97
2.19-2.220.34551480.2882922X-RAY DIFFRACTION97
2.22-2.250.28741120.29562078X-RAY DIFFRACTION69
2.25-2.290.36981510.28672925X-RAY DIFFRACTION97
2.29-2.330.37011580.28532934X-RAY DIFFRACTION97
2.33-2.370.29791300.27532868X-RAY DIFFRACTION96
2.37-2.420.29551520.2562946X-RAY DIFFRACTION97
2.42-2.470.28121690.26412928X-RAY DIFFRACTION98
2.47-2.520.27511720.27092924X-RAY DIFFRACTION98
2.52-2.580.31351720.26632959X-RAY DIFFRACTION98
2.58-2.640.32411470.26612935X-RAY DIFFRACTION98
2.64-2.710.2965940.25961812X-RAY DIFFRACTION60
2.71-2.790.29221560.26912934X-RAY DIFFRACTION98
2.79-2.880.31631700.27462928X-RAY DIFFRACTION98
2.88-2.990.30131800.25522934X-RAY DIFFRACTION98
2.99-3.110.291430.24462967X-RAY DIFFRACTION98
3.11-3.250.34431500.23582986X-RAY DIFFRACTION98
3.25-3.420.27081380.23372874X-RAY DIFFRACTION97
3.45-3.630.22351100.21182526X-RAY DIFFRACTION97
3.63-3.910.24481310.18952217X-RAY DIFFRACTION74
3.91-4.310.17051620.16042896X-RAY DIFFRACTION96
4.31-4.930.18191440.14472884X-RAY DIFFRACTION96
4.93-6.210.20711340.16393025X-RAY DIFFRACTION99
6.21-48.190.19581630.15422940X-RAY DIFFRACTION98

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