[English] 日本語
Yorodumi
- PDB-4qly: Crystal structure of CLA-ER, a novel enone reductase catalyzing a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4qly
TitleCrystal structure of CLA-ER, a novel enone reductase catalyzing a key step of a gut-bacterial fatty acid saturation metabolism, biohydrogenation
ComponentsEnone reductase CLA-ER
KeywordsOXIDOREDUCTASE / NADH oxidase/flavin reductase family / enone reductase / FMN
Function / homology
Function and homology information


Oxidoreductases / oxidoreductase activity / nucleotide binding
Similarity search - Function
NADH Oxidase / NADH Oxidase / Nitroreductase / Nitroreductase family / Nitroreductase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / NAD(P)H nitroreductase YodC
Similarity search - Component
Biological speciesLactobacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.005 Å
AuthorsHou, F. / Miyakawa, T. / Tanokura, M.
CitationJournal: Febs J. / Year: 2015
Title: Structure and reaction mechanism of a novel enone reductase.
Authors: Hou, F. / Miyakawa, T. / Kitamura, N. / Takeuchi, M. / Park, S.B. / Kishino, S. / Ogawa, J. / Tanokura, M.
History
DepositionJun 13, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references
Revision 1.2Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _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
Revision 1.3Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Enone reductase CLA-ER
B: Enone reductase CLA-ER
C: Enone reductase CLA-ER
D: Enone reductase CLA-ER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,6298
Polymers97,8034
Non-polymers1,8254
Water6,449358
1
A: Enone reductase CLA-ER
B: Enone reductase CLA-ER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8144
Polymers48,9022
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8080 Å2
ΔGint-55 kcal/mol
Surface area17700 Å2
MethodPISA
2
C: Enone reductase CLA-ER
D: Enone reductase CLA-ER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8144
Polymers48,9022
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8130 Å2
ΔGint-53 kcal/mol
Surface area17520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.710, 60.913, 72.561
Angle α, β, γ (deg.)85.57, 98.92, 111.62
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Enone reductase CLA-ER


Mass: 24450.818 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum (bacteria) / Strain: AKU 1009a / Gene: cla-er / Production host: Escherichia coli (E. coli) / References: UniProt: U6C5W9
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / 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: 2.06 Å3/Da / Density % sol: 40.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1M Bis-Tris, 21%(w/v) PEG monomethyl ether 5000, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 50917 / % possible obs: 96.8 % / Redundancy: 3.83 % / Biso Wilson estimate: 25.35 Å2 / Net I/σ(I): 17.52
Reflection shellResolution: 2→2.06 Å / Redundancy: 2.28 % / Mean I/σ(I) obs: 2.35 / % possible all: 84.2

-
Processing

Software
NameVersionClassification
MOLREPphasing
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KQB

1kqb


Resolution: 2.005→19.895 Å / SU ML: 0.24 / σ(F): 1.98 / Phase error: 26.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2261 1989 3.91 %
Rwork0.1729 48912 -
obs0.175 50901 97.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.01 Å2 / Biso mean: 32.2559 Å2 / Biso min: 12.47 Å2
Refinement stepCycle: LAST / Resolution: 2.005→19.895 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6624 0 124 358 7106
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086908
X-RAY DIFFRACTIONf_angle_d1.0419404
X-RAY DIFFRACTIONf_chiral_restr0.0411040
X-RAY DIFFRACTIONf_plane_restr0.0051204
X-RAY DIFFRACTIONf_dihedral_angle_d14.7292488
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0053-2.05540.3371300.28073152328288
2.0554-2.11090.28291410.23193462360397
2.1109-2.1730.26811360.21043544368097
2.173-2.2430.33171410.19753457359897
2.243-2.32310.25641500.19153487363797
2.3231-2.41590.26031440.18253510365497
2.4159-2.52570.26231430.18743518366198
2.5257-2.65850.25271390.18813497363698
2.6585-2.82470.25641490.18353507365698
2.8247-3.04210.27781390.1833568370798
3.0421-3.34690.2291500.17533536368699
3.3469-3.82820.20041380.15563563370199
3.8282-4.81180.15781460.13743542368899
4.8118-19.89630.18521430.15193569371299

+
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