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- PDB-7lej: Crystal structure of the second bromodomain (BD2) of human BRDT b... -

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Basic information

Entry
Database: PDB / ID: 7lej
TitleCrystal structure of the second bromodomain (BD2) of human BRDT bound to Volasertib
ComponentsBromodomain testis-specific protein
KeywordsGENE REGULATION / BRDT / BET / PLK1 / testis specific / Bromodomain
Function / homology
Function and homology information


sperm DNA condensation / male meiotic nuclear division / regulation of RNA splicing / male meiosis I / histone H4 reader activity / : / RNA splicing / mRNA processing / histone binding / transcription coactivator activity ...sperm DNA condensation / male meiotic nuclear division / regulation of RNA splicing / male meiosis I / histone H4 reader activity / : / RNA splicing / mRNA processing / histone binding / transcription coactivator activity / chromatin remodeling / protein serine/threonine kinase activity / chromatin binding / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / nucleus
Similarity search - Function
Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site ...Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily
Similarity search - Domain/homology
Chem-IBI / Bromodomain testis-specific protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 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
DepositionJan 14, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 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)14,9042
Polymers14,2851
Non-polymers6191
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.910, 72.910, 50.310
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 14285.423 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-IBI / N-{trans-4-[4-(cyclopropylmethyl)piperazin-1-yl]cyclohexyl}-4-{[(7R)-7-ethyl-5-methyl-8-(1-methylethyl)-6-oxo-5,6,7,8-tetrahydropteridin-2-yl]amino}-3-methoxybenzamide / Volasertib


Mass: 618.813 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H50N8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.84 Å3/Da / Density % sol: 56.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Magnesium acetate tetrahydrate, 0.1 M sodium cacodylate trihydrate (pH 6.5), 20 % w/v PEG 8,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 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: 1 Å / Relative weight: 1
ReflectionResolution: 1.73→36.455 Å / Num. obs: 16418 / % possible obs: 99.8 % / Redundancy: 10.848 % / Biso Wilson estimate: 32.97 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rrim(I) all: 0.048 / Χ2: 1.021 / Net I/σ(I): 29.71 / Num. measured all: 178097 / Scaling rejects: 40
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.73-1.7711.1490.4676.5413423120912040.9660.48999.6
1.77-1.8211.0920.3658.1612601114211360.9750.38299.5
1.82-1.8811.0790.27610.1112696115111460.9850.28999.6
1.88-1.9311.0260.20812.9412106110010980.9920.21899.8
1.93-211.1240.15915.911925107310720.9950.16799.9
2-2.0711.0950.12519.8211539104310400.9960.13199.7
2.07-2.1511.0460.08626.0611156101110100.9980.09199.9
2.15-2.2311.0060.07229.64104349489480.9980.075100
2.23-2.3310.9420.06432.39104399549540.9990.068100
2.33-2.4510.9040.05735.296178828820.9990.06100
2.45-2.5810.9730.05139.0892288418410.9980.054100
2.58-2.7410.80.04742.0486728048030.9990.0599.9
2.74-2.9210.6660.04246.5981177617610.9990.045100
2.92-3.1610.5210.0448.7676707307290.9990.04299.9
3.16-3.4610.4390.03652.666296366350.9990.03899.8
3.46-3.8710.3450.03455.0762596056050.9990.036100
3.87-4.4710.3640.03256.854415265250.9990.03399.8
4.47-5.4710.1980.03255.7846304544540.9990.034100
5.47-7.749.880.03254.735373583580.9980.034100
7.74-36.4559.1150.04153.919782192170.9980.04499.1

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VBQ

5vbq


Resolution: 1.73→36.455 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2105 998 6.08 %
Rwork0.1906 15416 -
obs0.1919 16414 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.31 Å2 / Biso mean: 34.2483 Å2 / Biso min: 15.79 Å2
Refinement stepCycle: final / Resolution: 1.73→36.455 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms994 0 45 68 1107
Biso mean--49.83 38.88 -
Num. residues----121
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7301-1.82130.24351380.2074214599
1.8213-1.93540.2331410.20562185100
1.9354-2.08480.25681410.21582173100
2.0848-2.29460.24231430.20322196100
2.2946-2.62650.22471420.19912194100
2.6265-3.30880.21831440.19822221100
3.3088-36.450.17981490.17252302100
Refinement TLS params.Method: refined / Origin x: 15.0678 Å / Origin y: -30.3345 Å / Origin z: 6.4723 Å
111213212223313233
T0.2566 Å2-0.119 Å2-0.0213 Å2-0.2223 Å20.0036 Å2--0.1677 Å2
L0.7868 °2-0.3721 °20.194 °2-3.4404 °2-1.507 °2--1.3238 °2
S-0.1883 Å °0.113 Å °0.0069 Å °-0.5003 Å °0.2287 Å °0.0221 Å °0.121 Å °-0.0429 Å °-0.0411 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA257 - 377
2X-RAY DIFFRACTION1allI1
3X-RAY DIFFRACTION1allQ1 - 76

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