[English] 日本語
Yorodumi
- PDB-5oji: Crystal structure of the dehydrogenase/reductase SDR family membe... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5oji
TitleCrystal structure of the dehydrogenase/reductase SDR family member 4 (DHRS4) from Caenorhabditis elegans
ComponentsDehydrogenase/reductase SDR family member 4
KeywordsOXIDOREDUCTASE / dehydrogenase SDR biotransformation
Function / homology
Function and homology information


RA biosynthesis pathway / carbonyl reductase (NADPH) / carbonyl reductase (NADPH) activity / catalytic activity
Similarity search - Function
Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ISATIN / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dehydrogenase/reductase SDR family member 4
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsScheidig, A.J. / Faust, A. / Ebert, B. / Maser, E. / Kisiela, M.
CitationJournal: FEBS J. / Year: 2018
Title: Crystal structure and catalytic characterization of the dehydrogenase/reductase SDR family member 4 (DHRS4) from Caenorhabditis elegans.
Authors: Kisiela, M. / Faust, A. / Ebert, B. / Maser, E. / Scheidig, A.J.
History
DepositionJul 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dehydrogenase/reductase SDR family member 4
B: Dehydrogenase/reductase SDR family member 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0276
Polymers55,2452
Non-polymers1,7814
Water10,251569
1
A: Dehydrogenase/reductase SDR family member 4
B: Dehydrogenase/reductase SDR family member 4
hetero molecules

A: Dehydrogenase/reductase SDR family member 4
B: Dehydrogenase/reductase SDR family member 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,05312
Polymers110,4914
Non-polymers3,5628
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area21390 Å2
ΔGint-76 kcal/mol
Surface area33450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.750, 94.750, 132.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11B-615-

HOH

-
Components

#1: Protein Dehydrogenase/reductase SDR family member 4


Mass: 27622.740 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: dhrs-4, F54F3.4 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G5EGA6, carbonyl reductase (NADPH)
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-ISN / ISATIN


Mass: 147.131 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H5NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 569 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 10% (w/v) PEG 8000 200 mM NaCl 100 mM K/Na-phosphate, pH 6.2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.976261 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976261 Å / Relative weight: 1
ReflectionResolution: 1.6→66.28 Å / Num. obs: 79504 / % possible obs: 99.3 % / Redundancy: 25 % / Biso Wilson estimate: 23.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.181 / Rrim(I) all: 0.185 / Net I/σ(I): 16.8
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 14 % / Rmerge(I) obs: 0.963 / CC1/2: 0.272 / Rrim(I) all: 0.998 / % possible all: 89.2

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3O4R

3o4r


Resolution: 1.6→66.28 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2294 3976 5 %RANDOM
Rwork0.2017 ---
obs0.2031 79503 99.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→66.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3880 0 118 582 4580
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064120
X-RAY DIFFRACTIONf_angle_d1.2065603
X-RAY DIFFRACTIONf_dihedral_angle_d17.0072454
X-RAY DIFFRACTIONf_chiral_restr0.053645
X-RAY DIFFRACTIONf_plane_restr0.005708
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5998-1.61930.43821160.41132203X-RAY DIFFRACTION83
1.6193-1.63980.42481420.41712688X-RAY DIFFRACTION100
1.6398-1.66140.40811400.39462675X-RAY DIFFRACTION100
1.6614-1.68420.35731400.38852651X-RAY DIFFRACTION100
1.6842-1.70830.39071420.37242688X-RAY DIFFRACTION100
1.7083-1.73380.35171410.33962693X-RAY DIFFRACTION100
1.7338-1.76080.3341410.33952678X-RAY DIFFRACTION100
1.7608-1.78970.35871410.32792685X-RAY DIFFRACTION100
1.7897-1.82060.32041410.31242662X-RAY DIFFRACTION100
1.8206-1.85370.36561410.31232684X-RAY DIFFRACTION100
1.8537-1.88930.29561420.27692696X-RAY DIFFRACTION100
1.8893-1.92790.28411420.24972693X-RAY DIFFRACTION100
1.9279-1.96980.22061410.22062687X-RAY DIFFRACTION100
1.9698-2.01570.22631420.20382703X-RAY DIFFRACTION100
2.0157-2.06610.24251420.19282688X-RAY DIFFRACTION100
2.0661-2.12190.22941420.18392701X-RAY DIFFRACTION100
2.1219-2.18440.20731410.17082692X-RAY DIFFRACTION100
2.1844-2.25490.22641430.1662699X-RAY DIFFRACTION100
2.2549-2.33550.20111420.16252702X-RAY DIFFRACTION100
2.3355-2.4290.18941430.16162720X-RAY DIFFRACTION100
2.429-2.53950.23351420.16342701X-RAY DIFFRACTION100
2.5395-2.67340.19151440.15412728X-RAY DIFFRACTION100
2.6734-2.84090.18241430.15062721X-RAY DIFFRACTION100
2.8409-3.06030.2011450.16242753X-RAY DIFFRACTION100
3.0603-3.36830.18341450.15172752X-RAY DIFFRACTION100
3.3683-3.85560.16951460.14582787X-RAY DIFFRACTION100
3.8556-4.85740.161480.13092808X-RAY DIFFRACTION100
4.8574-66.33690.19511580.17922989X-RAY DIFFRACTION100

+
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://pdbjlvh1.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