[English] 日本語
Yorodumi
- PDB-9d71: Crystal structure of Human Prostaglandin reductase 1 (PTGR1) in c... -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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
#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

-
Experimental details

-
Experiment

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

-
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.

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more