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

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Basic information

Entry
Database: PDB / ID: 7lel
TitleCrystal structure of the second bromodomain (BD2) of human BRDT bound to Bromosporine
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 reader activity / RNA splicing / lysine-acetylated histone binding / mRNA processing / histone binding / transcription coactivator activity ...sperm DNA condensation / male meiotic nuclear division / regulation of RNA splicing / male meiosis I / histone reader activity / RNA splicing / lysine-acetylated histone binding / mRNA processing / histone binding / transcription coactivator activity / chromatin remodeling / protein serine/threonine kinase activity / positive regulation of gene expression / chromatin binding / 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 / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily
Similarity search - Domain/homology
Bromosporine / Bromodomain testis-specific protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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
Revision 1.4Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_close_contact / struct_conn
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bromodomain testis-specific protein
B: Bromodomain testis-specific protein
C: Bromodomain testis-specific protein
D: Bromodomain testis-specific protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4378
Polymers54,8194
Non-polymers1,6184
Water1,76598
1
A: Bromodomain testis-specific protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1092
Polymers13,7051
Non-polymers4041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Bromodomain testis-specific protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1092
Polymers13,7051
Non-polymers4041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Bromodomain testis-specific protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1092
Polymers13,7051
Non-polymers4041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Bromodomain testis-specific protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1092
Polymers13,7051
Non-polymers4041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.990, 58.460, 60.770
Angle α, β, γ (deg.)72.580, 71.280, 70.620
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 13704.791 Da / Num. of mol.: 4
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-BMF / Bromosporine / ethyl (3-methyl-6-{4-methyl-3-[(methylsulfonyl)amino]phenyl}[1,2,4]triazolo[4,3-b]pyridazin-8-yl)carbamate


Mass: 404.444 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H20N6O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.6 Å3/Da / Density % sol: 52.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.05 M CaCl2, 2H2O, 0.1 M Bis-tris (pH 6.5), and 30 % v/v PEG MME 550

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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: 2.15→56.199 Å / Num. obs: 28678 / % possible obs: 95.3 % / Redundancy: 3.849 % / Biso Wilson estimate: 29.99 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.085 / Rrim(I) all: 0.099 / Χ2: 0.974 / Net I/σ(I): 11.77 / Num. measured all: 110378 / Scaling rejects: 49
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
2.15-2.213.870.5852.748014223420710.8280.67992.7
2.21-2.273.8760.5383.027970218320560.8610.62494.2
2.27-2.333.8970.4353.577649209919630.8980.50493.5
2.33-2.43.8740.3624.27466205119270.9240.42194
2.4-2.483.8950.2934.987261196718640.9490.33994.8
2.48-2.573.8950.2475.667105193518240.9620.28694.3
2.57-2.673.9040.2156.36949186117800.9710.2595.6
2.67-2.783.9030.1677.96635178317000.9790.19495.3
2.78-2.93.850.139.586360172916520.9870.15195.5
2.9-3.043.8670.1111.416055162915660.9880.12796.1
3.04-3.213.8380.09113.245773155115040.9930.10697
3.21-3.43.8090.06717.915428146614250.9950.07897.2
3.4-3.633.8050.05420.985087137813370.9960.06397
3.63-3.933.7810.04624.564647128112290.9970.05495.9
3.93-4.33.7690.04325.784308118311430.9970.0596.6
4.3-4.813.7490.03827.213906107610420.9980.04496.8
4.81-5.553.8180.04126.5135169409210.9970.04898
5.55-6.83.7990.04225.2529678087810.9960.0596.7
6.8-9.623.7520.03329.9322256145930.9980.03996.6
9.62-56.1993.5230.02931.2110573383000.9980.03488.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VBQ

5vbq


Resolution: 2.15→56.199 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 25.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2324 1004 3.5 %
Rwork0.1833 27666 -
obs0.1851 28670 95.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.56 Å2 / Biso mean: 38.2794 Å2 / Biso min: 19.59 Å2
Refinement stepCycle: final / Resolution: 2.15→56.199 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3784 0 112 98 3994
Biso mean--32.77 34.27 -
Num. residues----456
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.15-2.26340.32231410.236388994
2.2634-2.40520.29671410.2212388594
2.4052-2.59090.29481410.2157390295
2.5909-2.85160.22731440.2096396496
2.8516-3.26420.28011460.2056401397
3.2642-4.11240.22841450.1655401397
4.1124-56.1990.16511460.1472400097
Refinement TLS params.Method: refined / Origin x: -25.9313 Å / Origin y: -7.2059 Å / Origin z: -38.2494 Å
111213212223313233
T0.2333 Å20.0105 Å20.0051 Å2-0.2396 Å2-0.003 Å2--0.2455 Å2
L0.5075 °20.0359 °20.185 °2-0.301 °2-0.3261 °2--0.4058 °2
S0.0053 Å °0.0066 Å °0.01 Å °-0.0147 Å °0.0085 Å °0.006 Å °0.0125 Å °-0.0142 Å °-0.0176 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA265 - 378
2X-RAY DIFFRACTION1allB265 - 378
3X-RAY DIFFRACTION1allC265 - 378
4X-RAY DIFFRACTION1allD265 - 378
5X-RAY DIFFRACTION1allI1 - 4
6X-RAY DIFFRACTION1allQ1 - 98

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