[English] 日本語
Yorodumi
- PDB-7csh: AtPrR2 with NADP+ and (+)pinoresinol -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7csh
TitleAtPrR2 with NADP+ and (+)pinoresinol
ComponentsPinoresinol reductase 2
KeywordsOXIDOREDUCTASE / AtPrR2 / NADP+ / (+)pinoresinol / PLANT PROTEIN
Function / homology
Function and homology information


(-)-pinoresinol reductase / pinoresinol reductase activity / lignan biosynthetic process / plasmodesma
Similarity search - Function
Phenylcoumaran benzylic ether reductase-like / : / NmrA-like domain / NmrA-like family / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Chem-GEC / Chem-NDP / Pinoresinol reductase 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59077503881 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 reductase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5663
Polymers35,4621
Non-polymers1,1042
Water9,224512
1
A: Pinoresinol reductase 2
hetero molecules

A: Pinoresinol reductase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1326
Polymers70,9252
Non-polymers2,2084
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5360 Å2
ΔGint-18 kcal/mol
Surface area25210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.001, 90.465, 117.562
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-920-

HOH

21A-973-

HOH

31A-996-

HOH

-
Components

#1: Protein Pinoresinol reductase 2 / AtPrR2 / (-)-pinoresinol reductase / Pinoresinol-lariciresinol reductase 2 / AtPLR2


Mass: 35462.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PRR2, PLR2, At4g13660, F18A5.50 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9SVP6, (-)-pinoresinol reductase
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GEC / 4-[(3S,3aR,6S,6aR)-6-(3-methoxy-4-oxidanyl-phenyl)-1,3,3a,4,6,6a-hexahydrofuro[3,4-c]furan-3-yl]-2-methoxy-phenol / (+)-pinoresinol


Mass: 358.385 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H22O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 512 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2.1 M DL malic acid, pH 7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9798 Å
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Mar 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.59→39.001 Å / Num. obs: 55657 / % possible obs: 99.7 % / Redundancy: 12.9 % / Biso Wilson estimate: 12.9230290314 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 20.7
Reflection shellResolution: 1.59→1.65 Å / Rmerge(I) obs: 0.475 / Num. unique obs: 5475

-
Processing

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

1qyd


Resolution: 1.59077503881→39.0005 Å / SU ML: 0.100466840733 / Cross valid method: FREE R-VALUE / σ(F): 1.34366837069 / Phase error: 16.7727272879
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.183481709616 1999 3.59164166232 %
Rwork0.155820890259 53658 -
obs0.156809859231 55657 99.3679812894 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.0389862033 Å2
Refinement stepCycle: LAST / Resolution: 1.59077503881→39.0005 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2449 0 74 512 3035
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01055097255692580
X-RAY DIFFRACTIONf_angle_d1.16053433043498
X-RAY DIFFRACTIONf_chiral_restr0.0638065363167388
X-RAY DIFFRACTIONf_plane_restr0.00510883361507441
X-RAY DIFFRACTIONf_dihedral_angle_d15.40545595841521
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5908-1.63060.2120491721021390.1899196315523728X-RAY DIFFRACTION98.1472081218
1.6306-1.67460.2006188715741420.1768741325343818X-RAY DIFFRACTION99.9495204442
1.6746-1.72390.1841142859811410.1668941092223791X-RAY DIFFRACTION99.872999746
1.7239-1.77960.2003143633171430.1699290999443826X-RAY DIFFRACTION99.7737556561
1.7796-1.84320.1851247092031400.1615117686173781X-RAY DIFFRACTION98.8653555219
1.8432-1.9170.1909601380851430.1558520024413821X-RAY DIFFRACTION100
1.917-2.00420.1863432175131430.1568964969513843X-RAY DIFFRACTION99.9749184851
2.0042-2.10990.1839155724941430.1535575985123828X-RAY DIFFRACTION99.8993710692
2.1099-2.2420.1907892645711420.159577966323826X-RAY DIFFRACTION99.2992992993
2.242-2.41510.1732068201591430.1551490574073834X-RAY DIFFRACTION99.9497361146
2.4151-2.65810.1809150693521450.1555579707943880X-RAY DIFFRACTION99.9751614506
2.6581-3.04260.1765907293261430.1637951820753855X-RAY DIFFRACTION99.5270102066
3.0426-3.83290.1782637550151460.1469624494983913X-RAY DIFFRACTION99.7787610619
3.8329-39.00050.180777230981460.1433394523723914X-RAY DIFFRACTION96.3455149502

+
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