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- PDB-9d6y: Crystal structure of Apo Human Prostaglandin reductase 1 (PTGR1) ... -

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Basic information

Entry
Database: PDB / ID: 9d6y
TitleCrystal structure of Apo Human Prostaglandin reductase 1 (PTGR1) (Orthorhombic C form)
ComponentsProstaglandin reductase 1
KeywordsOXIDOREDUCTASE / 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 ...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
Prostaglandin reductase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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 Apo Human Prostaglandin reductase 1 (PTGR1) (Orthorhombic C 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


Theoretical massNumber of molelcules
Total (without water)71,9372
Polymers71,9372
Non-polymers00
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-17 kcal/mol
Surface area27690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.707, 98.747, 177.534
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-414-

HOH

21A-490-

HOH

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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.: 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)+]
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O
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: 2.82 Å3/Da / Density % sol: 56.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Berkeley B3: 30% (w/v) PEG 3350, 100 mM Bis-Tris pH 6.5, 400 mM Sodium chloride. HosaA.00871.a.A2.PW39298 at 16.1 mg/mL. His tag cleaved with 3C protease. Plate 14264 well B3 Drop 1, Puck: PSL0114, 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: 2.35→44.85 Å / Num. obs: 34288 / % possible obs: 99.9 % / Redundancy: 9.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.038 / Rrim(I) all: 0.121 / Χ2: 0.99 / Net I/σ(I): 12.4 / Num. measured all: 339917
Reflection shellResolution: 2.35→2.43 Å / % possible obs: 99.9 % / Redundancy: 10.2 % / Rmerge(I) obs: 1.245 / Num. measured all: 33584 / Num. unique obs: 3303 / CC1/2: 0.783 / Rpim(I) all: 0.406 / Rrim(I) all: 1.311 / Χ2: 1 / Net I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
PHENIXdev_5421refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→44.85 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2479 1741 5.09 %
Rwork0.1989 --
obs0.2015 34236 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→44.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5012 0 0 153 5165
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035116
X-RAY DIFFRACTIONf_angle_d0.6026923
X-RAY DIFFRACTIONf_dihedral_angle_d13.2771895
X-RAY DIFFRACTIONf_chiral_restr0.046784
X-RAY DIFFRACTIONf_plane_restr0.005875
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.420.36251410.29372674X-RAY DIFFRACTION100
2.42-2.50.31441530.26112644X-RAY DIFFRACTION100
2.5-2.590.28941260.24132690X-RAY DIFFRACTION100
2.59-2.690.29921200.24332706X-RAY DIFFRACTION100
2.69-2.810.32661570.24542676X-RAY DIFFRACTION100
2.81-2.960.33181620.26822676X-RAY DIFFRACTION100
2.96-3.150.26931410.24432681X-RAY DIFFRACTION100
3.15-3.390.24571580.22282711X-RAY DIFFRACTION100
3.39-3.730.22871590.20862680X-RAY DIFFRACTION100
3.73-4.270.22021310.16532746X-RAY DIFFRACTION100
4.27-5.380.20591310.1512753X-RAY DIFFRACTION100
5.38-44.850.22981620.17682858X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
11.14550.38690.30970.86510.12151.1082-0.01910.10660.00950.01080.09550.0570.0391-0.07710.03270.4825-0.0072-0.04360.5721-0.0290.5258-80.2513-12.7799-28.4865
22.46850.42510.69531.40310.2450.9389-0.15070.2370.2546-0.11550.06150.1628-0.06940.04020.02380.4667-0.0722-0.0280.4539-0.01950.4297-65.06741.1587-28.0383
31.44930.32810.51031.38860.77813.03690.12530.17270.0912-0.1662-0.0121-0.0735-0.2850.0746-0.11310.43950.03580.04360.3862-0.01180.437-18.51131.1808-18.8669
42.9913-0.43370.43381.1564-0.45991.17430.11490.3882-0.3609-0.0094-0.04310.21190.1039-0.0885-0.06460.4291-0.0486-0.010.4026-0.13990.4674-39.8854-17.7371-19.7613
50.81240.629-1.18373.0587-2.18674.0218-0.12060.05940.1105-0.18740.0217-0.18620.2272-0.02840.07070.46060.0087-0.01210.4439-0.04930.5042-19.7919-14.2703-23.127
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 2 through 154 )
2X-RAY DIFFRACTION2chain 'B' and (resid 155 through 329 )
3X-RAY DIFFRACTION3chain 'A' and (resid 2 through 112 )
4X-RAY DIFFRACTION4chain 'A' and (resid 113 through 293 )
5X-RAY DIFFRACTION5chain 'A' and (resid 294 through 329 )

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