[English] 日本語
Yorodumi
- PDB-2zb3: Crystal structure of mouse 15-ketoprostaglandin delta-13-reductas... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2zb3
TitleCrystal structure of mouse 15-ketoprostaglandin delta-13-reductase in complex with NADPH
ComponentsProstaglandin reductase 2
KeywordsOXIDOREDUCTASE / Rossmann fold
Function / homology
Function and homology information


13,14-dehydro-15-oxoprostaglandin 13-reductase / 15-oxoprostaglandin 13-reductase [NAD(P)+] activity / prostaglandin metabolic process / mitochondrion / cytosol
Similarity search - Function
Prostaglandin reductase 2 / Oxidoreductase, N-terminal domain / Medium-chain dehydrogenase/reductase / N-terminal domain of oxidoreductase / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain ...Prostaglandin reductase 2 / Oxidoreductase, N-terminal domain / Medium-chain dehydrogenase/reductase / N-terminal domain of oxidoreductase / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / Prostaglandin reductase 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWu, Y.H. / Wang, A.H.J. / Ko, T.P. / Guo, R.T. / Hu, S.M. / Chuang, L.M.
CitationJournal: Structure / Year: 2008
Title: Structural basis for catalytic and inhibitory mechanisms of human prostaglandin reductase PTGR2.
Authors: Wu, Y.H. / Ko, T.P. / Guo, R.T. / Hu, S.M. / Chuang, L.M. / Wang, A.H.J.
History
DepositionOct 16, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Prostaglandin reductase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9442
Polymers38,1981
Non-polymers7451
Water8,359464
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Prostaglandin reductase 2
hetero molecules

A: Prostaglandin reductase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,8874
Polymers76,3972
Non-polymers1,4912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_553-y,-x,-z-3/21
Buried area4950 Å2
ΔGint-17 kcal/mol
Surface area27190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.829, 85.829, 100.906
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-401-

HOH

-
Components

#1: Protein Prostaglandin reductase 2 / PTGR2 / 15-oxoprostaglandin 13-reductase / Zinc-binding alcohol dehydrogenase domain-containing protein 1


Mass: 38198.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ptgr2, Zadh1 / Plasmid: pGEX4T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8VDQ1, 13,14-dehydro-15-oxoprostaglandin 13-reductase
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 464 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FEATURE OF UNIPROT (PTGR2_MOUSE, Q8VDQ1) SHOWS CONFLICT AT THIS POSITION: P -> T (IN REF. 1; BAB32284)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M cacodylate, pH6.5, 27% PEG 8000, 80mM Mg(OAc)2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 13, 2004 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 26149 / Num. obs: 24685 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 7.3 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 19.4
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.969 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2447 / % possible all: 96.1

-
Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1V3V

1v3v


Resolution: 2→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1119 -RANDOM
Rwork0.209 ---
all0.213 26103 --
obs0.213 23101 88.5 %-
Displacement parametersBiso mean: 33.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2620 0 48 464 3132
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_bond_d0.02
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.008
RfactorNum. reflection% reflection
Rfree0.35 94 -
Rwork0.318 --
obs-2101 82.4 %

+
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