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

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Basic information

Entry
Database: PDB / ID: 7lem
TitleCrystal structure of the first bromodomain (BD1) of human BRDT bound to LRRK2-IN-1
ComponentsBromodomain testis-specific protein
KeywordsGENE REGULATION / Bromodomain / LRRK / kinase
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-4K4 / Bromodomain testis-specific protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 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
B: Bromodomain testis-specific protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,40114
Polymers26,6392
Non-polymers1,76212
Water1,58588
1
A: Bromodomain testis-specific protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2007
Polymers13,3191
Non-polymers8816
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain testis-specific protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2007
Polymers13,3191
Non-polymers8816
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.220, 30.020, 72.840
Angle α, β, γ (deg.)90.000, 104.560, 90.000
Int Tables number4
Space group name H-MP1211

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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.: 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-4K4 / 2-[(2-methoxy-4-{[4-(4-methylpiperazin-1-yl)piperidin-1-yl]carbonyl}phenyl)amino]-5,11-dimethyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one


Mass: 570.685 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H38N8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.75 Å3/Da / Density % sol: 55.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M (NH4)2SO4, 0.1 M sodium cacodylate trihydrate (pH 6.5), and 30 % 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-ID / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.89→35.25 Å / Num. obs: 23495 / % possible obs: 98.7 % / Redundancy: 3.645 % / Biso Wilson estimate: 34.851 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Rrim(I) all: 0.051 / Χ2: 1.021 / Net I/σ(I): 17.14 / Num. measured all: 85628 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.89-1.943.6840.5092.6316700.8820.59997.7
1.94-1.993.690.3543.816860.9440.41698.2
1.99-2.053.6770.3094.2715930.9510.36398.6
2.05-2.113.7020.2335.6516050.9680.27399.5
2.11-2.183.6750.186.815250.9830.21297.4
2.18-2.263.6810.1528.0914660.9870.17898.8
2.26-2.343.6880.1249.7614540.9910.14698.6
2.34-2.443.6760.10910.5313780.9930.12898.9
2.44-2.553.6630.08113.3913570.9960.09599.1
2.55-2.673.640.06516.7512600.9970.07699.2
2.67-2.823.6590.05918.5512240.9970.07100
2.82-2.993.6510.04722.6211820.9980.05599.7
2.99-3.193.5890.04225.3310580.9980.0597.5
3.19-3.453.5920.03231.8810290.9990.03898.8
3.45-3.783.5890.02438.899430.9990.02898.8
3.78-4.233.5650.02343.358440.9990.02799.1
4.23-4.883.5990.0247.657630.9990.02399.3
4.88-5.983.5410.02144.846470.9990.02499.1
5.98-8.453.4980.01945.925100.9990.02298.8
8.45-35.253.2160.01648.773010.9990.0297.1

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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: 7L73

7l73


Resolution: 1.89→35.25 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 30.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2474 1198 5.1 %
Rwork0.2003 22289 -
obs0.2027 23487 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.96 Å2 / Biso mean: 44.6938 Å2 / Biso min: 18.85 Å2
Refinement stepCycle: final / Resolution: 1.89→35.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1806 0 124 88 2018
Biso mean--43.03 38.64 -
Num. residues----216
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.89-1.96550.34481290.2888239397
1.9655-2.05490.29011310.2522243299
2.0549-2.16330.26521320.2234245898
2.1633-2.29880.2671330.2116247299
2.2988-2.47620.25291320.2136245999
2.4762-2.72530.25271330.2096248099
2.7253-3.11950.26461340.21692487100
3.1195-3.92940.22551340.1898250499
3.9294-35.250.22651400.1697260499
Refinement TLS params.Method: refined / Origin x: -8.1012 Å / Origin y: -2.6173 Å / Origin z: -21.4932 Å
111213212223313233
T0.3363 Å20.0494 Å2-0.0268 Å2-0.205 Å2-0.0049 Å2--0.2623 Å2
L2.3959 °2-0.1904 °2-0.0794 °2-1.6556 °2-0.1525 °2--0.6987 °2
S-0.1214 Å °-0.3224 Å °0.0063 Å °0.5541 Å °0.1065 Å °-0.2039 Å °-0.0342 Å °0.0165 Å °0.02 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA29 - 136
2X-RAY DIFFRACTION1allB29 - 136
3X-RAY DIFFRACTION1allI1 - 2
4X-RAY DIFFRACTION1allQ1 - 98
5X-RAY DIFFRACTION1allD1 - 10

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