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- PDB-6bph: Crystal structure of the chromodomain of RBBP1 -

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Basic information

Entry
Database: PDB / ID: 6bph
TitleCrystal structure of the chromodomain of RBBP1
ComponentsAT-rich interactive domain-containing protein 4A
KeywordsUNKNOWN FUNCTION / Crystal structure of the chromodomain of RBBP1 / Structural Genomics / Structural Genomics Consortium / SGC
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 / SH3 type barrels. - #140 / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
AT-rich interactive domain-containing protein 4A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsLiu, Y. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Crystal structure of chromo barrel domain of RBBP1.
Authors: Lei, M. / Feng, Y. / Zhou, M. / Yang, Y. / Loppnau, P. / Li, Y. / Yang, Y. / Liu, Y.
History
DepositionNov 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 28, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)8,06818
Polymers8,0681
Non-polymers017
Water43224
1
A: AT-rich interactive domain-containing protein 4A

A: AT-rich interactive domain-containing protein 4A


Theoretical massNumber of molelcules
Total (without water)16,13636
Polymers16,1362
Non-polymers034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area1670 Å2
ΔGint-12 kcal/mol
Surface area8110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.493, 41.493, 81.349
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-702-

UNX

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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: 8068.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARID4A, RBBP1, RBP1 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE2 / References: UniProt: P29374
#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 17 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.17 Å3/Da / Density % sol: 43.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG 3350, 0.2M magnesium chloride, 0.1M HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Mar 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→36.97 Å / Num. obs: 7057 / % possible obs: 99.6 % / Redundancy: 13.1 % / Biso Wilson estimate: 25.03 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.02 / Rrim(I) all: 0.075 / Net I/σ(I): 26.2 / Num. measured all: 92703 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.8413.31.07751743900.9190.31.1193.398.8
9-36.978.70.0267288410.0090.02769.799.8

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2LCC

2lcc


Resolution: 1.85→36.9 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.909 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.15 / SU Rfree Blow DPI: 0.128 / SU Rfree Cruickshank DPI: 0.125
Details: ARP/WARP was used for automated model re-building. REFMAC during intermediate iterations of model refinement.
RfactorNum. reflection% reflection
Rfree0.226 312 4.79 %
Rwork0.206 --
obs0.207 6508 99.5 %
Displacement parametersBiso max: 85.75 Å2 / Biso mean: 31.08 Å2 / Biso min: 10.42 Å2
Baniso -1Baniso -2Baniso -3
1--4.1544 Å20 Å20 Å2
2---4.1544 Å20 Å2
3---8.3087 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: final / Resolution: 1.85→36.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms522 0 17 24 563
Biso mean--29.86 37.93 -
Num. residues----66
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d184SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes11HARMONIC2
X-RAY DIFFRACTIONt_gen_planes82HARMONIC5
X-RAY DIFFRACTIONt_it556HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion70SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact627SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d556HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg763HARMONIC20.95
X-RAY DIFFRACTIONt_omega_torsion3.49
X-RAY DIFFRACTIONt_other_torsion16.25
LS refinement shellResolution: 1.85→2.07 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.222 85 4.75 %
Rwork0.182 1703 -
all-1788 -
obs--98.95 %
Refinement TLS params.Method: refined / Origin x: 4.7367 Å / Origin y: 19.7027 Å / Origin z: 4.4266 Å
111213212223313233
T-0.0358 Å20.015 Å20.0203 Å2--0.0123 Å20.0308 Å2---0.046 Å2
L1.2508 °2-0.319 °2-0.503 °2-1.877 °2-0.74 °2--2.9854 °2
S0.0648 Å °0.0399 Å °0.0995 Å °0.0721 Å °0.0514 Å °0.0566 Å °-0.2011 Å °-0.1689 Å °-0.1162 Å °
Refinement TLS groupSelection details: { A|570 - A|635 }

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