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- PDB-7v8n: Crystal structure of the PWWP-ARID domain of ARID4A -

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Basic information

Entry
Database: PDB / ID: 7v8n
TitleCrystal structure of the PWWP-ARID domain of ARID4A
ComponentsAT-rich interactive domain-containing protein 4A
KeywordsDNA BINDING PROTEIN
Function / homology
Function and homology information


establishment of Sertoli cell barrier / genomic imprinting / negative regulation of stem cell population maintenance / : / positive regulation of stem cell population maintenance / erythrocyte development / transcription repressor complex / negative regulation of cell migration / HDACs deacetylate histones / negative regulation of transforming growth factor beta receptor signaling pathway ...establishment of Sertoli cell barrier / genomic imprinting / negative regulation of stem cell population maintenance / : / positive regulation of stem cell population maintenance / erythrocyte development / transcription repressor complex / negative regulation of cell migration / HDACs deacetylate histones / negative regulation of transforming growth factor beta receptor signaling pathway / spermatogenesis / Potential therapeutics for SARS / transcription by RNA polymerase II / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / plasma membrane
Similarity search - Function
: / : / RBB1NT / RBB1NT (NUC162) domain / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / ARID/BRIGHT DNA binding domain / ARID DNA-binding domain / ARID DNA-binding domain superfamily / ARID/BRIGHT DNA binding domain ...: / : / RBB1NT / RBB1NT (NUC162) domain / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / ARID/BRIGHT DNA binding domain / ARID DNA-binding domain / ARID DNA-binding domain superfamily / ARID/BRIGHT DNA binding domain / ARID domain profile. / BRIGHT, ARID (A/T-rich interaction domain) domain / Tudor domain / Tudor domain / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily
Similarity search - Domain/homology
AT-rich interactive domain-containing protein 4A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsWei, X. / Lin, L. / Lu, Q.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of the PWWP-ARID of ARID4A
Authors: Ren, D. / Wei, X. / Lin, L. / Liu, L. / Fan, Y. / Lu, Q. / He, G.
History
DepositionAug 23, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 31, 2022Provider: 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: AT-rich interactive domain-containing protein 4A
B: AT-rich interactive domain-containing protein 4A


Theoretical massNumber of molelcules
Total (without water)58,0592
Polymers58,0592
Non-polymers00
Water3,045169
1
A: AT-rich interactive domain-containing protein 4A


Theoretical massNumber of molelcules
Total (without water)29,0301
Polymers29,0301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AT-rich interactive domain-containing protein 4A


Theoretical massNumber of molelcules
Total (without water)29,0301
Polymers29,0301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.668, 54.818, 180.755
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein AT-rich interactive domain-containing protein 4A / ARID domain-containing protein 4A / Retinoblastoma-binding protein 1 / RBBP-1


Mass: 29029.580 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARID4A, RBBP1, RBP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P29374
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.33 Å3/Da / Density % sol: 47.27 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 2.4 M ammonium phosphate dibasic, 0.1 M Tris pH8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.05→46.87 Å / Num. obs: 34354 / % possible obs: 98.44 % / Redundancy: 12.46 % / Biso Wilson estimate: 33.06 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.107 / Rrim(I) all: 0.116 / Χ2: 0.946 / Net I/σ(I): 18.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.05-2.139.130.9072.329420.8150.96386.15
2.13-2.2111.420.7443.933700.9490.7897.97
2.21-2.3113.660.5576.934310.9860.579100
2.31-2.4313.450.447934420.9930.465100
2.43-2.5912.660.30712.134700.9930.32100
2.59-2.7913.610.21816.734630.9960.22699.97
2.79-3.0713.050.14521.934700.9970.151100
3.07-3.5112.870.0922935020.9980.096100
3.51-4.4212.320.06436.135330.9990.067100
4.42-46.8711.990.04842.137310.9990.05100

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LJX

4ljx


Resolution: 2.05→46.87 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 23.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2314 1994 5.81 %
Rwork0.1958 32351 -
obs0.1979 34345 98.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.06 Å2 / Biso mean: 34.8915 Å2 / Biso min: 15.76 Å2
Refinement stepCycle: final / Resolution: 2.05→46.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3420 0 0 169 3589
Biso mean---35.72 -
Num. residues----428
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.10.37561140.30311962207684
2.1-2.160.35121340.25212155228995
2.16-2.220.27371430.221722972440100
2.22-2.30.2561420.221323192461100
2.3-2.380.23681440.222423172461100
2.38-2.470.28611390.212622972436100
2.47-2.590.22911470.214423402487100
2.59-2.720.25511430.214423202463100
2.72-2.890.25031430.217923412484100
2.89-3.120.25351470.219423292476100
3.12-3.430.22761440.210523722516100
3.43-3.930.231470.176923722519100
3.93-4.940.17731510.153723942545100
4.95-46.870.20651560.172125362692100

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