[English] 日本語
Yorodumi
- PDB-6ie5: Crystal structure of ADCP1 tandem Agenet domain 3-4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ie5
TitleCrystal structure of ADCP1 tandem Agenet domain 3-4
ComponentsAgenet domain-containing protein
KeywordsTRANSLATION / Agenet domain
Function / homology
Function and homology information


DNA methylation-dependent constitutive heterochromatin formation / : / histone reader activity / chromosome, centromeric region / heterochromatin / histone binding / nucleus
Similarity search - Function
Agenet domain, plant type / Tudor-like domain present in plant sequences. / Agenet-like domain / Agenet domain
Similarity search - Domain/homology
Protein AGENET DOMAIN (AGD)-CONTAINING P1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.298 Å
AuthorsZhao, S. / Zhang, B. / Li, H.
CitationJournal: Cell Res. / Year: 2019
Title: ADCP1-tandem Agenet domain 1-2 in complex wit h H3K9me2
Authors: Zhao, S. / Zhang, B. / Li, H.
History
DepositionSep 13, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 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: Agenet domain-containing protein


Theoretical massNumber of molelcules
Total (without water)18,1661
Polymers18,1661
Non-polymers00
Water1,08160
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8410 Å2
Unit cell
Length a, b, c (Å)56.204, 56.204, 188.243
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-224-

HOH

21A-257-

HOH

-
Components

#1: Protein Agenet domain-containing protein / At1g09320


Mass: 18166.379 Da / Num. of mol.: 1 / Fragment: Agenet domain, UNP residues 201-355
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ADCP1 / Plasmid: pGEX6p / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q500V5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.37 Å3/Da / Density % sol: 48 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 2.1M DL-Malic acid pH 7.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 10, 2017 / Details: mirrors
RadiationMonochromator: double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 14873 / % possible obs: 99.8 % / Redundancy: 13.7 % / Biso Wilson estimate: 20.64 Å2 / Rmerge(I) obs: 0.204 / Rpim(I) all: 0.056 / Rrim(I) all: 0.211 / Χ2: 0.707 / Net I/σ(I): 3.8 / Num. measured all: 203552
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.3413.40.6627670.9550.1840.6880.429100
2.34-2.3813.10.6697280.9610.1880.6950.45100
2.38-2.4312.80.6097590.9630.1730.6330.459100
2.43-2.4811.90.5527140.9570.1620.5760.45199.7
2.48-2.5311.30.4937430.9630.1480.5150.45999.6
2.53-2.5913.60.57380.9740.1380.5190.449100
2.59-2.6614.50.487470.9840.1290.4970.474100
2.66-2.7314.70.4347360.9820.1150.4490.493100
2.73-2.8114.80.3617580.9830.0950.3730.53100
2.81-2.914.60.3047270.9870.0810.3140.55100
2.9-314.70.2467470.9930.0660.2550.635100
3-3.1214.60.2117660.9940.0560.2180.693100
3.12-3.2614.40.2027290.9940.0540.2090.728100
3.26-3.4414.30.1597370.9960.0430.1650.852100
3.44-3.65140.1477360.9960.040.1530.905100
3.65-3.9313.80.1277520.9960.0350.1321.047100
3.93-4.3313.30.117480.9970.0310.1151.113100
4.33-4.9511.30.0977320.9970.0290.1011.21899.2
4.95-6.2414.80.1167570.9980.0310.121.02199.9
6.24-5013.70.0967520.9980.0260.11.18898.4

-
Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.298→38.459 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0.77 / Phase error: 21.95 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2228 691 4.66 %
Rwork0.2012 14129 -
obs0.2022 14820 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.47 Å2 / Biso mean: 17.9083 Å2 / Biso min: 2.38 Å2
Refinement stepCycle: final / Resolution: 2.298→38.459 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1145 0 0 60 1205
Biso mean---19.12 -
Num. residues----141
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071174
X-RAY DIFFRACTIONf_angle_d1.1071587
X-RAY DIFFRACTIONf_chiral_restr0.042165
X-RAY DIFFRACTIONf_plane_restr0.004206
X-RAY DIFFRACTIONf_dihedral_angle_d14.161433
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.298-2.47540.34841290.286228342963
2.4754-2.72450.2891330.269728202953
2.7245-3.11860.23051340.190528602994
3.1186-3.92840.2111610.169527842945
3.9284-38.46480.15851340.171928312965

+
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