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- PDB-5vbq: CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRDT IN COMPL... -

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Basic information

Entry
Database: PDB / ID: 5vbq
TitleCRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRDT IN COMPLEX WITH BI2536
ComponentsBromodomain testis-specific protein
KeywordsTRANSCRIPTION/INHIBITOR / BROMODOMAIN / CAP / HUNK1 / MCAP / PROTEIN BINDING-INHIBITOR COMPLEX / MITOTIC CHROMOSOME ASSOCIATED PROTEIN / INHIBITOR / TRANSCRIPTION-INHIBITOR COMPLEX
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-R78 / Bromodomain testis-specific protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsEMBER, S.W. / ZHU, J.-Y. / SCHONBRUNN, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)HD076542-01S1 United States
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
DepositionMar 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 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 1.3Oct 4, 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

Downloads & links

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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)28,71121
Polymers26,6392
Non-polymers2,07219
Water3,423190
1
A: Bromodomain testis-specific protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,49713
Polymers13,3191
Non-polymers1,17812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain testis-specific protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2138
Polymers13,3191
Non-polymers8947
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.590, 31.000, 69.470
Angle α, β, γ (deg.)90.000, 96.900, 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 / Fragment: UNP RESIDUES 29-137
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRDT / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) STAR / References: UniProt: Q58F21
#2: Chemical ChemComp-R78 / 4-{[(7R)-8-cyclopentyl-7-ethyl-5-methyl-6-oxo-5,6,7,8-tetrahydropteridin-2-yl]amino}-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide


Mass: 521.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H39N7O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O

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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: 2.66 Å3/Da / Density % sol: 53.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 8 MG/ML BRDT, 25MM HEPES PH 7.5, 75MM SODIUM CHLORIDE, 0.5MM DTT, 50MM MES PH 6.5, 0.1M AMMONIUM, SULFATE, 15% PEG MME 5,000, 10% DMSO, 1 MM BI2536

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 17, 2016
RadiationMonochromator: ROSENBAUM-ROCK DOUBLE-CRYSTAL si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→34.484 Å / Num. obs: 33699 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 3.662 % / Biso Wilson estimate: 17.39 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.052 / Rrim(I) all: 0.061 / Χ2: 0.999 / Net I/σ(I): 17.23
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.65-1.693.6580.3954.9524820.8850.46499.4
1.69-1.743.6760.3315.9823970.9120.38899.7
1.74-1.793.7030.326.4623520.9170.37499.7
1.79-1.843.7130.2737.7822910.9360.31999.7
1.84-1.913.7160.1939.8722010.9730.22699.6
1.91-1.973.7210.1512.2421510.9820.17599.6
1.97-2.053.7130.11414.1420850.990.13399.6
2.05-2.133.720.08816.6719770.9920.10399.5
2.13-2.223.710.07118.6219200.9950.08399.3
2.22-2.333.7090.06220.1718340.9960.07399.5
2.33-2.463.6920.05721.6517230.9950.06798.7
2.46-2.613.6780.04923.6216480.9970.05798.9
2.61-2.793.6580.04525.9115690.9960.05399
2.79-3.013.6460.03927.1714370.9980.04699
3.01-3.33.5780.03629.4913280.9970.04398.3
3.3-3.693.5670.03531.7311840.9980.04197.8
3.69-4.263.5130.03233.6910730.9970.03897.5
4.26-5.223.5060.02934.529190.9980.03498
5.22-7.383.4080.03233.367140.9970.03898.1
7.38-34.4843.0870.03532.524140.9960.04296.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
SERGUIdata collection
PHENIX1.9_1692refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KCX

4kcx


Resolution: 1.65→34.484 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 16.09
RfactorNum. reflection% reflection
Rfree0.1718 1347 4 %
Rwork0.1435 --
obs-33695 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 198.55 Å2 / Biso mean: 31.0779 Å2 / Biso min: 8.54 Å2
Refinement stepCycle: final / Resolution: 1.65→34.484 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1850 0 315 190 2355
Biso mean--34.21 32.97 -
Num. residues----224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012033
X-RAY DIFFRACTIONf_angle_d1.3972721
X-RAY DIFFRACTIONf_chiral_restr0.053281
X-RAY DIFFRACTIONf_plane_restr0.007334
X-RAY DIFFRACTIONf_dihedral_angle_d19.01825
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.7090.20371320.17013184331699
1.709-1.77740.20271350.159732263361100
1.7774-1.85830.19661340.15932123346100
1.8583-1.95620.16831350.142632403375100
1.9562-2.07880.16951340.138532243358100
2.0788-2.23930.18061340.13253232336699
2.2393-2.46460.1771340.14283207334199
2.4646-2.8210.18651360.14333267340399
2.821-3.55360.18821350.14713227336299
3.5536-34.49120.13981380.13853329346797
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.72780.34210.45624.9722-0.24092.1979-0.08040.154-0.1663-0.1404-0.0254-0.80720.15550.52840.0220.15250.012-0.01320.2076-0.0030.36320.4659-6.3107-2.2938
22.56571.4927-0.79983.1413-0.07211.4310.04-0.17580.10640.120.0056-0.1807-0.15680.0702-0.00290.11380.0056-0.02180.1056-0.02510.1634-18.0733-1.07950.4877
36.49240.3115-1.72451.069-0.42433.1171-0.02740.2156-0.04940.01690.056-0.06950.2527-0.1562-0.00330.1326-0.01650.0090.0690.00860.1457-28.7946-13.3959-4.6849
46.0929-1.9343.55551.3319-0.88943.25660.05740.0629-0.1260.00310.013-0.22430.15460.157-0.0810.1064-0.0029-0.0050.0688-0.00860.1602-13.1034-10.7928-5.0283
56.1429-3.8996-0.29563.3679-1.81354.51050.25670.06140.1028-0.6288-0.00520.6233-0.4523-0.8555-0.20930.230.0421-0.03380.16410.00860.1251-30.6801-1.5008-13.8396
62.2696-0.9049-0.17172.1450.01892.93430.13440.22220.4763-0.0515-0.0698-0.2973-0.13120.3631-0.04370.1689-0.03980.01450.1352-0.01180.1832-11.92541.1977-9.7076
75.69612.2133-1.09713.8298-3.89674.27350.14840.11840.29130.0025-0.0515-1.082-0.06831.13570.02060.2103-0.00980.05130.5638-0.15720.62233.0691-5.8281-23.9571
83.84912.57412.93.96280.36116.82880.16340.4131-0.4612-0.24370.3715-0.90630.09840.6076-0.42420.260.04410.05080.3389-0.13270.2834-6.9224-13.2715-29.894
96.2837-4.62742.6483.4443-2.08193.05070.17310.3544-0.0765-0.5804-0.1296-0.15330.17470.2855-0.03040.2659-0.0240.03340.2098-0.04830.1497-18.3454-10.4821-32.2991
105.8381.71023.51483.43673.40044.0566-0.1102-0.1236-0.0081-0.06610.24740.0609-0.1251-0.3052-0.16020.29080.0243-0.01870.1990.04440.1378-30.8117-1.7665-33.5644
118.8058-0.32440.75082.2272-0.19292.2281-0.08640.3380.3095-0.30580.0483-0.4892-0.41280.39060.04550.2523-0.08260.04680.18760.0050.213-12.18480.8106-28.0672
126.5970.20540.43581.9415-0.03712.89820.03610.08480.1935-0.04610.0796-0.335-0.06580.3239-0.12050.1828-0.0022-0.00350.1483-0.0410.177-14.9631-4.0035-20.8672
137.64742.5015-2.08174.1527-4.62665.24290.12850.1396-0.09430.56460.04070.82270.6342-0.7718-0.14150.3443-0.06210.05010.189-0.00530.1583-29.757-11.5553-20.6346
142.47820.97813.21562.74760.04265.02270.09290.016-0.1574-0.04760.0006-0.51680.20590.5426-0.09550.24620.07150.0020.2347-0.06490.2404-10.3521-14.1328-20.0376
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 25 through 37 )A25 - 37
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 57 )A38 - 57
3X-RAY DIFFRACTION3chain 'A' and (resid 58 through 75 )A58 - 75
4X-RAY DIFFRACTION4chain 'A' and (resid 76 through 108 )A76 - 108
5X-RAY DIFFRACTION5chain 'A' and (resid 109 through 113 )A109 - 113
6X-RAY DIFFRACTION6chain 'A' and (resid 114 through 136 )A114 - 136
7X-RAY DIFFRACTION7chain 'B' and (resid 25 through 37 )B25 - 37
8X-RAY DIFFRACTION8chain 'B' and (resid 38 through 45 )B38 - 45
9X-RAY DIFFRACTION9chain 'B' and (resid 46 through 57 )B46 - 57
10X-RAY DIFFRACTION10chain 'B' and (resid 58 through 65 )B58 - 65
11X-RAY DIFFRACTION11chain 'B' and (resid 66 through 90 )B66 - 90
12X-RAY DIFFRACTION12chain 'B' and (resid 91 through 108 )B91 - 108
13X-RAY DIFFRACTION13chain 'B' and (resid 109 through 113 )B109 - 113
14X-RAY DIFFRACTION14chain 'B' and (resid 114 through 136 )B114 - 136

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