[English] 日本語
Yorodumi
- PDB-4koq: Crystal Structure of WHY3 from Arabidopsis thaliana -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4koq
TitleCrystal Structure of WHY3 from Arabidopsis thaliana
ComponentsSingle-stranded DNA-binding protein WHY3, chloroplastic
KeywordsDNA BINDING PROTEIN / Plant / Whirly / SINGLE-STRANDED DNA BINDING PROTEIN
Function / homology
Function and homology information


salicylic acid mediated signaling pathway / chloroplast nucleoid / DNA repair complex / chloroplast stroma / chloroplast / defense response / single-stranded DNA binding / DNA repair / mRNA binding / regulation of DNA-templated transcription ...salicylic acid mediated signaling pathway / chloroplast nucleoid / DNA repair complex / chloroplast stroma / chloroplast / defense response / single-stranded DNA binding / DNA repair / mRNA binding / regulation of DNA-templated transcription / mitochondrion / DNA binding
Similarity search - Function
Whirly transcription factor / Whirly transcription factor / Transcriptional Coactivator Pc4; Chain A / ssDNA-binding transcriptional regulator / Transcriptional Co-activator pc4; Chain A / Roll / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Single-stranded DNA-binding protein WHY3, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsCappadocia, L. / Parent, J.S. / Brisson, N. / Sygusch, J.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: A family portrait: structural comparison of the Whirly proteins from Arabidopsis thaliana and Solanum tuberosum.
Authors: Cappadocia, L. / Parent, J.S. / Sygusch, J. / Brisson, N.
History
DepositionMay 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Single-stranded DNA-binding protein WHY3, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2103
Polymers20,0201
Non-polymers1902
Water1,76598
1
A: Single-stranded DNA-binding protein WHY3, chloroplastic
hetero molecules

A: Single-stranded DNA-binding protein WHY3, chloroplastic
hetero molecules

A: Single-stranded DNA-binding protein WHY3, chloroplastic
hetero molecules

A: Single-stranded DNA-binding protein WHY3, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,84012
Polymers80,0804
Non-polymers7608
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_445-y-1/2,x-1/2,z1
crystal symmetry operation4_545y+1/2,-x-1/2,z1
Buried area12690 Å2
ΔGint-163 kcal/mol
Surface area32070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.600, 80.600, 63.622
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-461-

HOH

21A-471-

HOH

-
Components

#1: Protein Single-stranded DNA-binding protein WHY3, chloroplastic / Protein PLASTID TRANSCRIPTIONALLY ACTIVE 11 / Protein WHIRLY 3 / AtWHY3


Mass: 20019.957 Da / Num. of mol.: 1 / Fragment: UNP residues 78-246
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: Col-0 / Gene: At2g02740, PTAC11, T20F6.12, WHY3 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q66GR6
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsISOFORM-2 HAS BEEN CRYSTALLIZED AND THIS RESIDUE IS MISSING IN ISOFORM-2

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 14% PEG 1000, 0.2M Potassium Acetate, 0.1M Sodium Citrate pH 4.2, vapor diffusion, hanging drop, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 16, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 18616 / Num. obs: 18616 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.4 % / Rmerge(I) obs: 0.093 / Χ2: 1.131 / Net I/σ(I): 8.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.85-1.9210.20.92618120.923199.7
1.92-1.99130.69118220.9091100
1.99-2.0814.20.51218281.031100
2.08-2.1914.20.35618331.082199.9
2.19-2.3314.30.25418281.1421100
2.33-2.5114.20.18918481.2181100
2.51-2.7614.10.13218481.2671100
2.76-3.1613.80.09718631.3071100
3.16-3.9913.30.06919091.2521100
3.99-5012.60.04320251.11100

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→42.451 Å / Occupancy max: 1 / Occupancy min: 0.6 / FOM work R set: 0.8556 / SU ML: 0.18 / σ(F): 1.34 / Phase error: 20.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2263 1858 10 %RANDOM
Rwork0.189 ---
obs0.1928 18587 99.69 %-
all-18616 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.81 Å2 / Biso mean: 42.8812 Å2 / Biso min: 15.17 Å2
Refinement stepCycle: LAST / Resolution: 1.85→42.451 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1323 0 10 98 1431
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121366
X-RAY DIFFRACTIONf_angle_d1.3551849
X-RAY DIFFRACTIONf_chiral_restr0.088200
X-RAY DIFFRACTIONf_plane_restr0.006236
X-RAY DIFFRACTIONf_dihedral_angle_d13.015492
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.89430.27531360.26011216135296
1.8943-1.950.25591400.22112631403100
1.95-2.0130.26081400.199612741414100
2.013-2.08490.23911390.193712491388100
2.0849-2.16840.22871410.180612711412100
2.1684-2.26710.19091420.176912671409100
2.2671-2.38660.20711410.172912811422100
2.3866-2.53610.21391430.172412801423100
2.5361-2.73190.21141420.169912821424100
2.7319-3.00680.20741430.17812951438100
3.0068-3.44170.22491450.178412991444100
3.4417-4.33550.2241480.176413321480100
4.3355-42.4510.24271580.215914201578100

+
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