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- PDB-7xpj: crystal structure of rice ASI1 BAH domain -

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Basic information

Entry
Database: PDB / ID: 7xpj
Titlecrystal structure of rice ASI1 BAH domain
ComponentsBAH domain-containing protein
KeywordsGENE REGULATION / BAH domain / ASI1 / rice / SUVH6 / H3K9me2 deposition
Function / homology
Function and homology information


nucleic acid binding / chromatin binding
Similarity search - Function
Bromo adjacent homology (BAH) domain / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / BAH domain profile. / RNA-binding domain superfamily / SH3 type barrels. / Roll / Nucleotide-binding alpha-beta plait domain superfamily / Mainly Beta
Similarity search - Domain/homology
BAH domain-containing protein
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.301 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BAH domain-containing protein


Theoretical massNumber of molelcules
Total (without water)18,8001
Polymers18,8001
Non-polymers00
Water1,45981
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.327, 107.327, 73.362
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-277-

HOH

21A-281-

HOH

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Components

#1: Protein BAH domain-containing protein


Mass: 18799.529 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.24 Å3/Da / Density % sol: 62.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.8 M ammonium sulfate and 0.1 M bicine, pH 9.0

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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: 2.3→50 Å / Num. obs: 11548 / % possible obs: 100 % / Redundancy: 37.6 % / CC1/2: 0.985 / Rmerge(I) obs: 0.188 / Net I/σ(I): 18.7
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 38.5 % / Rmerge(I) obs: 1.246 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 555 / CC1/2: 0.936 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AV4

3av4


Resolution: 2.301→30.983 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2357 550 4.78 %
Rwork0.2225 --
obs0.2231 11508 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.301→30.983 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1275 0 0 81 1356
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021303
X-RAY DIFFRACTIONf_angle_d0.5131756
X-RAY DIFFRACTIONf_dihedral_angle_d15.213784
X-RAY DIFFRACTIONf_chiral_restr0.044188
X-RAY DIFFRACTIONf_plane_restr0.003226
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3013-2.53280.30871270.27812671X-RAY DIFFRACTION100
2.5328-2.89910.25231320.25332699X-RAY DIFFRACTION100
2.8991-3.65160.24941500.22662706X-RAY DIFFRACTION100
3.6516-30.980.20361410.19812882X-RAY DIFFRACTION100

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