[English] 日本語
Yorodumi
- PDB-5ldg: Isopiperitenone reductase from Mentha piperita in complex with Is... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ldg
TitleIsopiperitenone reductase from Mentha piperita in complex with Isopiperitenone and NADP
Components(-)-isopiperitenone reductase
KeywordsOXIDOREDUCTASE / short-chain dehydrogenases/reductases (SDR) / Rossmann fold / Isopiperitenone / Isopulegone
Function / homology
Function and homology information


(-)-isopiperitenone reductase / menthol biosynthetic process / (-)-isopiperitenone reductase activity / terpene metabolic process / NADPH binding / membrane / cytoplasm
Similarity search - Function
short chain dehydrogenase / 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
(-)-Isopiperitenone / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / (-)-isopiperitenone reductase
Similarity search - Component
Biological speciesMentha piperita (peppermint)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsKaruppiah, V. / Toogood, H.S. / Leys, D. / Scrutton, N.S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/J015512/1 and BB/M000354/1 United Kingdom
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2016
Title: Pinpointing a Mechanistic Switch Between Ketoreduction and "Ene" Reduction in Short-Chain Dehydrogenases/Reductases.
Authors: Lygidakis, A. / Karuppiah, V. / Hoeven, R. / Ni Cheallaigh, A. / Leys, D. / Gardiner, J.M. / Toogood, H.S. / Scrutton, N.S.
History
DepositionJun 26, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 10, 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: (-)-isopiperitenone reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4733
Polymers34,5801
Non-polymers8942
Water9,962553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-4 kcal/mol
Surface area13380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.560, 65.490, 95.109
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein (-)-isopiperitenone reductase


Mass: 34579.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mentha piperita (peppermint) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6WAU1, (-)-isopiperitenone reductase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-IT9 / (-)-Isopiperitenone


Mass: 150.218 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 553 / 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: 2.73 Å3/Da / Density % sol: 54.9 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.06M Divalents (0.3M Magnesium chloride hexahydrate; 0.3M Calcium chloride dihydrate), 0.1M Buffer system 3 pH 8.5 (1M Tris (base); BICINE), 50% Precipitant Mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 31, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.3→60.56 Å / Num. obs: 92810 / % possible obs: 99.2 % / Redundancy: 6 % / CC1/2: 0.987 / Rmerge(I) obs: 0.103 / Net I/σ(I): 11.4
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 5.1 / % possible all: 98.2

-
Processing

Software
NameVersionClassification
PHENIX(dev_2386: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3O26

3o26


Resolution: 1.3→53.939 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 11.13
RfactorNum. reflection% reflection
Rfree0.1456 2006 2.16 %
Rwork0.1198 --
obs0.1203 92733 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.3→53.939 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2397 0 59 553 3009
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112690
X-RAY DIFFRACTIONf_angle_d1.1213692
X-RAY DIFFRACTIONf_dihedral_angle_d12.7761078
X-RAY DIFFRACTIONf_chiral_restr0.092416
X-RAY DIFFRACTIONf_plane_restr0.008503
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.33250.15351340.11566341X-RAY DIFFRACTION98
1.3325-1.36860.14341450.10366305X-RAY DIFFRACTION98
1.3686-1.40880.13091540.10196390X-RAY DIFFRACTION99
1.4088-1.45430.12951310.10316363X-RAY DIFFRACTION98
1.4543-1.50630.16391350.11776408X-RAY DIFFRACTION99
1.5063-1.56660.11081530.09036420X-RAY DIFFRACTION99
1.5666-1.63790.1161330.08596418X-RAY DIFFRACTION99
1.6379-1.72430.11541440.08726441X-RAY DIFFRACTION99
1.7243-1.83230.12051410.09776500X-RAY DIFFRACTION100
1.8323-1.97380.12211440.10366501X-RAY DIFFRACTION100
1.9738-2.17240.12981490.10726552X-RAY DIFFRACTION100
2.1724-2.48680.1371440.11346552X-RAY DIFFRACTION100
2.4868-3.1330.16351460.13396650X-RAY DIFFRACTION100
3.133-53.98580.17531530.14976886X-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://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