[English] 日本語
Yorodumi
- PDB-7cs2: Apo structure of dimeric IiPLR1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7cs2
TitleApo structure of dimeric IiPLR1
ComponentsPinoresinol-lariciresinol reductase
KeywordsOXIDOREDUCTASE / PLR1 / dimer / PLANT PROTEIN
Function / homologypinoresinol reductase activity / lignan biosynthetic process / Phenylcoumaran benzylic ether reductase-like / : / NmrA-like domain / NmrA-like family / NAD(P)-binding domain superfamily / nucleotide binding / Pinoresinol-lariciresinol reductase
Function and homology information
Biological speciesIsatis tinctoria (woad)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68800468428 Å
AuthorsShao, K. / Zhang, P.
CitationJournal: Nat Commun / Year: 2021
Title: Structure-based engineering of substrate specificity for pinoresinol-lariciresinol reductases.
Authors: Xiao, Y. / Shao, K. / Zhou, J. / Wang, L. / Ma, X. / Wu, D. / Yang, Y. / Chen, J. / Feng, J. / Qiu, S. / Lv, Z. / Zhang, L. / Zhang, P. / Chen, W.
History
DepositionAug 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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: Pinoresinol-lariciresinol reductase
C: Pinoresinol-lariciresinol reductase
B: Pinoresinol-lariciresinol reductase
D: Pinoresinol-lariciresinol reductase
E: Pinoresinol-lariciresinol reductase
F: Pinoresinol-lariciresinol reductase


Theoretical massNumber of molelcules
Total (without water)213,9766
Polymers213,9766
Non-polymers00
Water1,63991
1
A: Pinoresinol-lariciresinol reductase
C: Pinoresinol-lariciresinol reductase


Theoretical massNumber of molelcules
Total (without water)71,3252
Polymers71,3252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-8 kcal/mol
Surface area25410 Å2
MethodPISA
2
B: Pinoresinol-lariciresinol reductase
D: Pinoresinol-lariciresinol reductase


Theoretical massNumber of molelcules
Total (without water)71,3252
Polymers71,3252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-7 kcal/mol
Surface area25590 Å2
MethodPISA
3
E: Pinoresinol-lariciresinol reductase
F: Pinoresinol-lariciresinol reductase


Theoretical massNumber of molelcules
Total (without water)71,3252
Polymers71,3252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-8 kcal/mol
Surface area25580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.758, 242.458, 77.562
Angle α, β, γ (deg.)90.000, 110.532, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

#1: Protein
Pinoresinol-lariciresinol reductase / IiPLR1


Mass: 35662.586 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Isatis tinctoria (woad) / Production host: Escherichia coli (E. coli) / References: UniProt: I6LRS1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 3.06 Å3/Da / Density % sol: 59.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 0.2M sodium citrate tribasic, 0.1 M sodium citrate/citric acid, pH 4.0, 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.688→31.399 Å / Num. obs: 70443 / % possible obs: 99.5 % / Redundancy: 6.7 % / Biso Wilson estimate: 66.1630245508 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 19.8
Reflection shellResolution: 2.69→2.78 Å / Rmerge(I) obs: 0.764 / Num. unique obs: 6742

-
Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QYD

1qyd


Resolution: 2.68800468428→31.3980458407 Å / SU ML: 0.348769881523 / Cross valid method: FREE R-VALUE / σ(F): 1.35349369364 / Phase error: 26.4830188047
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.241548783356 1996 2.83349658589 %
Rwork0.200523743192 68447 -
obs0.201731584446 70443 98.9645967969 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.4566911034 Å2
Refinement stepCycle: LAST / Resolution: 2.68800468428→31.3980458407 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13755 0 0 91 13846
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.010149096729513992
X-RAY DIFFRACTIONf_angle_d1.1558747658718903
X-RAY DIFFRACTIONf_chiral_restr0.06116862907372165
X-RAY DIFFRACTIONf_plane_restr0.006054269574772413
X-RAY DIFFRACTIONf_dihedral_angle_d16.71929858444
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.688005-2.75520.3169591835071340.2633153192424612X-RAY DIFFRACTION93.2783018868
2.7552-2.82960.2905842671131380.2673958270314856X-RAY DIFFRACTION99.5217218015
2.8296-2.91280.3542812311051490.2574532717884927X-RAY DIFFRACTION99.587992937
2.9128-3.00680.2716464442651400.2419585118094896X-RAY DIFFRACTION99.6044303797
3.0068-3.11420.2966574194061450.2411501950134937X-RAY DIFFRACTION99.6275240149
3.1142-3.23870.3028519095751440.2542521405894926X-RAY DIFFRACTION99.6266457064
3.2387-3.3860.298113306761470.2385542685844940X-RAY DIFFRACTION99.725544011
3.386-3.56420.2978295511451370.2363672266964829X-RAY DIFFRACTION98.590430812
3.5642-3.78720.2732180905431380.212253162184899X-RAY DIFFRACTION99.2903607333
3.7872-4.0790.188839081931420.2011590412274880X-RAY DIFFRACTION98.5478806907
4.079-4.48850.1948008958131450.1628938912594923X-RAY DIFFRACTION99.8620689655
4.4885-5.13550.2415338204461450.1639628726494963X-RAY DIFFRACTION99.9217527387
5.1355-6.4610.2384368596911450.1939366079024948X-RAY DIFFRACTION99.7649363369
6.461-31.398040.1974474525771470.1719716412764911X-RAY DIFFRACTION98.5580670304

+
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