[English] 日本語
Yorodumi
- PDB-7xpk: crystal structure of rice ASI1 BAH domain in complex with a rice ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7xpk
Titlecrystal structure of rice ASI1 BAH domain in complex with a rice SUVH6 peptide
Components
  • Alpha-aminoacylpeptide hydrolase
  • BAH domain-containing protein
KeywordsGENE REGULATION / BAH domain / ASI1 / rice / SUVH6 / H3K9me2 deposition
Function / homology
Function and homology information


: / : / metallopeptidase activity / chromosome / nucleic acid binding / chromatin binding / endoplasmic reticulum / proteolysis / zinc ion binding / membrane / nucleus
Similarity search - Function
Histone H3-K9 methyltransferase, plant / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / SRA-YDG / SRA-YDG superfamily / SAD/SRA domain / YDG domain profile. / SET and RING finger associated domain. Domain of unknown function in SET domain containing proteins and in Deinococcus radiodurans DRA1533. / Aminopeptidase N-type / ERAP1-like C-terminal domain / ERAP1-like C-terminal domain ...Histone H3-K9 methyltransferase, plant / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / SRA-YDG / SRA-YDG superfamily / SAD/SRA domain / YDG domain profile. / SET and RING finger associated domain. Domain of unknown function in SET domain containing proteins and in Deinococcus radiodurans DRA1533. / Aminopeptidase N-type / ERAP1-like C-terminal domain / ERAP1-like C-terminal domain / Pre-SET domain / Pre-SET motif / Pre-SET domain profile. / N-terminal to some SET domains / Bromo adjacent homology (BAH) domain superfamily / Bromo adjacent homology (BAH) domain / BAH domain / BAH domain profile. / Post-SET domain / Post-SET domain profile. / Aminopeptidase N-like , N-terminal domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Peptidase family M1 domain / Peptidase M1 N-terminal domain / Aminopeptidase N-like , N-terminal domain superfamliy / PUA-like superfamily / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / Peptidase M4/M1, CTD superfamily / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Alpha-aminoacylpeptide hydrolase / BAH domain-containing protein
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsYuan, J. / Du, J.
Funding support China, 1items
OrganizationGrant numberCountry
Other governmentJCYJ20200109110403829 China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Molecular basis of locus-specific H3K9 methylation catalyzed by SUVH6 in plants.
Authors: Zhang, J. / Yuan, J. / Lin, J. / Chen, L. / You, L.Y. / Chen, S. / Peng, L. / Wang, C.H. / Du, J. / Duan, C.G.
History
DepositionMay 4, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BAH domain-containing protein
B: Alpha-aminoacylpeptide hydrolase
C: BAH domain-containing protein
D: Alpha-aminoacylpeptide hydrolase


Theoretical massNumber of molelcules
Total (without water)40,4234
Polymers40,4234
Non-polymers00
Water5,188288
1
A: BAH domain-containing protein
B: Alpha-aminoacylpeptide hydrolase


Theoretical massNumber of molelcules
Total (without water)20,2112
Polymers20,2112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-6 kcal/mol
Surface area10020 Å2
MethodPISA
2
C: BAH domain-containing protein
D: Alpha-aminoacylpeptide hydrolase


Theoretical massNumber of molelcules
Total (without water)20,2112
Polymers20,2112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-5 kcal/mol
Surface area10020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.715, 72.939, 76.581
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein BAH domain-containing protein


Mass: 18136.811 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: OsJ_02569 / Plasmid: pMBP / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: B9EY07
#2: Protein/peptide Alpha-aminoacylpeptide hydrolase


Mass: 2074.500 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Oryza sativa Japonica Group (Japanese rice)
References: UniProt: A0A0E0IIA9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.07 Å3/Da / Density % sol: 40.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 30% PEG400 and 0.1 M CHES, pH 9.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 22, 2020
RadiationMonochromator: silicon crystal (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 31676 / % possible obs: 99.8 % / Redundancy: 6.5 % / CC1/2: 1 / Rmerge(I) obs: 0.098 / Net I/σ(I): 19
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.837 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2996 / CC1/2: 0.712 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7XPJ

7xpj


Resolution: 1.8→38.291 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2339 1599 5.05 %
Rwork0.1996 --
obs0.2013 31676 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→38.291 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2831 0 0 288 3119
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032892
X-RAY DIFFRACTIONf_angle_d0.6783888
X-RAY DIFFRACTIONf_dihedral_angle_d17.4641758
X-RAY DIFFRACTIONf_chiral_restr0.05413
X-RAY DIFFRACTIONf_plane_restr0.004500
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8560.31561690.28342646X-RAY DIFFRACTION99
1.856-1.92240.34791450.26082702X-RAY DIFFRACTION100
1.9224-1.99930.29351370.24622690X-RAY DIFFRACTION100
1.9993-2.09030.26361220.24292730X-RAY DIFFRACTION100
2.0903-2.20050.27011720.23152678X-RAY DIFFRACTION100
2.2005-2.33840.26861700.21912686X-RAY DIFFRACTION100
2.3384-2.51890.26421250.22562727X-RAY DIFFRACTION100
2.5189-2.77230.23741460.22462750X-RAY DIFFRACTION100
2.7723-3.17330.23711590.20252737X-RAY DIFFRACTION100
3.1733-3.99730.21671380.17042792X-RAY DIFFRACTION100
3.9973-38.290.17081160.16482939X-RAY DIFFRACTION99

+
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://pdbjlvh1.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