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

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Basic information

Entry
Database: PDB / ID: 7bjy
TitleCrystal structure of the first bromodomain (BD1) of human BRDT bound to Ro3280
ComponentsIsoform 2 of Bromodomain testis-specific protein
KeywordsGENE REGULATION / Bromodomain / kinase / Ro3280
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-like ...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-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-79C / Bromodomain testis-specific protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 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: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 24, 2021Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: 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: Isoform 2 of Bromodomain testis-specific protein
B: Isoform 2 of Bromodomain testis-specific protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8506
Polymers26,6392
Non-polymers1,2114
Water68538
1
A: Isoform 2 of Bromodomain testis-specific protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8632
Polymers13,3191
Non-polymers5441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Isoform 2 of Bromodomain testis-specific protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9874
Polymers13,3191
Non-polymers6683
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.040, 57.040, 407.870
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Isoform 2 of Bromodomain testis-specific protein / Cancer/testis antigen 9 / CT9 / RING3-like protein


Mass: 13319.365 Da / Num. of mol.: 2
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-79C / 4-[(9-cyclopentyl-7,7-difluoro-5-methyl-6-oxo-6,7,8,9-tetrahydro-5H-pyrimido[4,5-b][1,4]diazepin-2-yl)amino]-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide


Mass: 543.609 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H35F2N7O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 3.6 Å3/Da / Density % sol: 65.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M NaCl, 0.1 M Bis-Tris pH5.5, 25% w/v PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.22→42.254 Å / Num. obs: 20864 / % possible obs: 99.9 % / Redundancy: 21.146 % / Biso Wilson estimate: 46.06 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.132 / Rrim(I) all: 0.135 / Χ2: 1.098 / Net I/σ(I): 19.24 / Num. measured all: 441196 / Scaling rejects: 180
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
2.22-2.2820.2661.113330420150115010.8311.141100
2.28-2.3420.7641.0183.2929568142514240.8151.04399.9
2.34-2.4121.0860.8753.9630195143214320.9130.896100
2.41-2.4821.550.725.1930106139813970.9350.73799.9
2.48-2.5621.9470.5797.0428817131413130.9720.59299.9
2.56-2.6522.2380.5187.9928731129312920.9690.5399.9
2.65-2.7522.5680.41110.3328549126512650.9820.421100
2.75-2.8722.6890.34412.5727749122412230.9850.35299.9
2.87-2.9922.8450.27815.1326797117311730.9950.284100
2.99-3.1422.3760.19720.8424837111011100.9960.202100
3.14-3.3122.0740.16323.9423928108510840.9970.16799.9
3.31-3.5121.4820.11531.0421869101910180.9980.11899.9
3.51-3.7520.7050.09535.73199609649640.9980.098100
3.75-4.0519.9030.08140.19182719189180.9980.083100
4.05-4.4419.5870.07342.75166108488480.9980.075100
4.44-4.9619.2460.0743.32149357767760.9980.072100
4.96-5.7319.4820.06841.2137937087080.9990.07100
5.73-7.0219.5120.05940.9118246066060.9990.061100
7.02-9.9318.3220.04347.22921650350310.044100
9.93-42.25416.2490.0345.17502131330910.03198.7

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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: 7L73

7l73


Resolution: 2.22→42.254 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 23.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2555 1099 5.27 %
Rwork0.2152 19761 -
obs0.2174 20860 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.63 Å2 / Biso mean: 53.4485 Å2 / Biso min: 27.96 Å2
Refinement stepCycle: final / Resolution: 2.22→42.254 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1830 0 86 38 1954
Biso mean--71.48 47.43 -
Num. residues----220
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.22-2.3210.30121320.25222365
2.321-2.44340.35011330.2662390
2.4434-2.59650.27541350.24232438
2.5965-2.79690.28161330.2492379
2.7969-3.07830.3621350.25992443
3.0783-3.52350.23611380.23722474
3.5235-4.43850.2311410.18142526
4.4385-42.2540.2191520.18792746
Refinement TLS params.Method: refined / Origin x: 13.256 Å / Origin y: 14.0217 Å / Origin z: 15.4455 Å
111213212223313233
T0.5726 Å20.1312 Å2-0.0121 Å2-0.2549 Å2-0.0115 Å2--0.3456 Å2
L0.8324 °2-1.3588 °2-0.8873 °2-3.0693 °21.3403 °2--1.5113 °2
S-0.2946 Å °-0.226 Å °-0.0439 Å °0.2882 Å °0.3069 Å °0.1675 Å °-0.0191 Å °0.1016 Å °-0.006 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA29 - 136
2X-RAY DIFFRACTION1allB25 - 136
3X-RAY DIFFRACTION1allI1 - 2
4X-RAY DIFFRACTION1allQ1 - 40
5X-RAY DIFFRACTION1allE1 - 2

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