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- PDB-7l73: Crystal structure of the first bromodomain (BD1) of human BRDT bo... -

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Basic information

Entry
Database: PDB / ID: 7l73
TitleCrystal structure of the first bromodomain (BD1) of human BRDT bound to ERK5-IN-1
ComponentsBromodomain testis-specific protein
KeywordsGENE REGULATION / BRDT / BET / PLK1 / testis specific
Function / homology
Function and homology information


sperm DNA condensation / male meiotic nuclear division / male meiosis I / regulation of RNA splicing / histone reader activity / RNA splicing / lysine-acetylated histone binding / mRNA processing / histone binding / transcription coactivator activity ...sperm DNA condensation / male meiotic nuclear division / male meiosis I / regulation of RNA splicing / histone reader activity / RNA splicing / lysine-acetylated histone binding / mRNA processing / histone binding / transcription coactivator activity / chromatin remodeling / regulation of DNA-templated transcription / positive regulation of gene expression / nucleus
Similarity search - Function
Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. ...Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily
Similarity search - Domain/homology
Chem-VYJ / Bromodomain testis-specific protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsChan, A. / Karim, M.R. / Schonbrunn, E.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Differential BET Bromodomain Inhibition by Dihydropteridinone and Pyrimidodiazepinone Kinase Inhibitors.
Authors: Karim, R.M. / Bikowitz, M.J. / Chan, A. / Zhu, J.Y. / Grassie, D. / Becker, A. / Berndt, N. / Gunawan, S. / Lawrence, N.J. / Schonbrunn, E.
History
DepositionDec 25, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 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: Bromodomain testis-specific protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5973
Polymers13,3191
Non-polymers1,2782
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.370, 23.570, 58.450
Angle α, β, γ (deg.)90.000, 104.660, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Bromodomain testis-specific protein / Cancer/testis antigen 9 / CT9 / RING3-like protein


Mass: 13319.365 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRDT / Production host: Escherichia coli (E. coli) / References: UniProt: Q58F21
#2: Chemical ChemComp-VYJ / 11-cyclopentyl-2-({2-ethoxy-4-[4-(4-methylpiperazin-1-yl)piperidine-1-carbonyl]phenyl}amino)-5-methyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one


Mass: 638.802 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C36H46N8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.11 Å3/Da / Density % sol: 41.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.05 M (NH4)2SO4, 0.05 M Bis-tris (pH 6.5), and 30 % Pentaerythritol ethoxylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.46→40.812 Å / Num. obs: 19695 / % possible obs: 99.4 % / Redundancy: 3.497 % / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rrim(I) all: 0.052 / Χ2: 1.02 / Net I/σ(I): 17.67 / Num. measured all: 68881 / Scaling rejects: 5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.46-1.53.3390.4073.114290.8460.48699.9
1.5-1.543.3830.3233.9214030.90.38699.6
1.54-1.583.5080.2854.7413670.9220.33899.9
1.58-1.633.5340.2265.8713360.9440.26899.7
1.63-1.693.5550.1797.1813190.9620.21299.6
1.69-1.753.5440.1448.4712130.9780.17100
1.75-1.813.5680.1210.4712290.9840.14199.9
1.81-1.883.5580.09413.2111380.9890.11199.8
1.88-1.973.5430.06916.5111470.9940.08299.1
1.97-2.063.5390.05620.2610470.9960.066100
2.06-2.183.5110.04624.1810200.9970.05599
2.18-2.313.5390.03927.59650.9980.04699.2
2.31-2.473.5250.03828.368970.9980.04599.7
2.47-2.673.5330.03332.148590.9980.03999.4
2.67-2.923.4870.03134.687980.9980.03699
2.92-3.263.4990.02737.66980.9980.03199.4
3.26-3.773.4780.02341.516170.9990.02798.2
3.77-4.623.4620.02143.935410.9990.02497
4.62-6.533.3920.02141.954240.9990.02599.3
6.53-40.8123.1490.0242.672480.9990.02496.1

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.11.1-2575_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VBQ

5vbq


Resolution: 1.46→40.812 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 18.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1903 1001 5.08 %
Rwork0.1695 18694 -
obs0.1706 19695 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 41.34 Å2 / Biso mean: 16.22 Å2 / Biso min: 6.79 Å2
Refinement stepCycle: final / Resolution: 1.46→40.812 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms925 0 94 163 1182
Biso mean--16.31 24.92 -
Num. residues----112
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061053
X-RAY DIFFRACTIONf_angle_d1.071431
X-RAY DIFFRACTIONf_chiral_restr0.064141
X-RAY DIFFRACTIONf_plane_restr0.005172
X-RAY DIFFRACTIONf_dihedral_angle_d19.803434
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.46-1.53680.26531400.21062617100
1.5368-1.63310.20381420.18292654100
1.6331-1.75920.17761430.1772670100
1.7592-1.93630.2211410.17482643100
1.9363-2.21640.18511430.16112661100
2.2164-2.79240.20381440.175269499
2.7924-40.810.16741480.1585275599

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