[English] 日本語
Yorodumi
- PDB-1qyd: Crystal structures of pinoresinol-lariciresinol and phenylcoumara... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qyd
TitleCrystal structures of pinoresinol-lariciresinol and phenylcoumaran benzylic ether reductases, and their relationship to isoflavone reductases
Componentspinoresinol-lariciresinol reductase
KeywordsPLANT PROTEIN / NADPH-dependent aromatic alcohol reductases / PCBER / PLR / IFR / lignans / isoflavonoids
Function / homology
Function and homology information


(-)-lariciresinol reductase / lariciresinol reductase activity / (-)-pinoresinol catabolic process / (+)-pinoresinol catabolic process / (-)-lariciresinol catabolic process / (-)-lariciresinol biosynthetic process / (+)-lariciresinol biosynthetic process / (+)-secoisolariciresinol biosynthetic process / (+)-pinoresinol reductase / (-)-pinoresinol reductase ...(-)-lariciresinol reductase / lariciresinol reductase activity / (-)-pinoresinol catabolic process / (+)-pinoresinol catabolic process / (-)-lariciresinol catabolic process / (-)-lariciresinol biosynthetic process / (+)-lariciresinol biosynthetic process / (+)-secoisolariciresinol biosynthetic process / (+)-pinoresinol reductase / (-)-pinoresinol reductase / lignan biosynthetic process / pinoresinol reductase activity
Similarity search - Function
Phenylcoumaran benzylic ether reductase-like / : / NmrA-like domain / NmrA-like family / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold ...Phenylcoumaran benzylic ether reductase-like / : / NmrA-like domain / NmrA-like family / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / 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
Bifunctional pinoresinol-lariciresinol reductase 1
Similarity search - Component
Biological speciesThuja plicata (giant arborvitae)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMin, T. / Kasahara, H. / Bedgar, D.L. / Youn, B. / Lawrence, P.K. / Gang, D.R. / Halls, S.C. / Park, H. / Hilsenbeck, J.L. / Davin, L.B. / Kang, C.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Crystal structures of pinoresinol-lariciresinol and phenylcoumaran benzylic ether reductases and their relationship to isoflavone reductases.
Authors: Min, T. / Kasahara, H. / Bedgar, D.L. / Youn, B. / Lawrence, P.K. / Gang, D.R. / Halls, S.C. / Park, H. / Hilsenbeck, J.L. / Davin, L.B. / Lewis, N.G. / Kang, C.
History
DepositionSep 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: pinoresinol-lariciresinol reductase
B: pinoresinol-lariciresinol reductase
C: pinoresinol-lariciresinol reductase
D: pinoresinol-lariciresinol reductase


Theoretical massNumber of molelcules
Total (without water)142,4964
Polymers142,4964
Non-polymers00
Water1,53185
1
A: pinoresinol-lariciresinol reductase
C: pinoresinol-lariciresinol reductase


Theoretical massNumber of molelcules
Total (without water)71,2482
Polymers71,2482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: pinoresinol-lariciresinol reductase
D: pinoresinol-lariciresinol reductase


Theoretical massNumber of molelcules
Total (without water)71,2482
Polymers71,2482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.574, 125.959, 128.578
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
pinoresinol-lariciresinol reductase


Mass: 35624.059 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thuja plicata (giant arborvitae) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: Q9LD14
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.35 Å3/Da / Density % sol: 47.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: PEG 8000, MES, NaCl, Ca Acetate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 %PEG80001reservoir
20.1 MMES1reservoirpH6.2
30.1 M1reservoirNaCl
40.1 Mcalcium acetate1reservoir
520 mMTris1droppH8.0
61 mMEDTA1drop
75 mMdithiothreitol1drop
850 mg/mlprotein1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.95 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 10, 2001
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.5→10 Å / Num. all: 33210 / Num. obs: 33210 / % possible obs: 79 % / Observed criterion σ(I): 0
Reflection
*PLUS
Lowest resolution: 10 Å / Num. measured all: 36439

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→10 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1681 5 %RANDOM
Rwork0.193 ---
all0.251 33210 --
obs0.235 31529 --
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9987 0 0 85 10072
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_deg3.54
Refinement
*PLUS
Lowest resolution: 10 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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