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

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Basic information

Entry
Database: PDB / ID: 7lek
TitleCrystal structure of the second bromodomain (BD2) of human BRDT bound to ERK5-IN-1
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-VYJ / Bromodomain testis-specific protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.75 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

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)57,47210
Polymers54,8194
Non-polymers2,6536
Water1,00956
1
A: Bromodomain testis-specific protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3442
Polymers13,7051
Non-polymers6391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain testis-specific protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3793
Polymers13,7051
Non-polymers6742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Bromodomain testis-specific protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4063
Polymers13,7051
Non-polymers7012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Bromodomain testis-specific protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3442
Polymers13,7051
Non-polymers6391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.610, 99.320, 60.400
Angle α, β, γ (deg.)90.000, 108.390, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-402-

CL

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 267 or resid 269 through 270...
21(chain B and (resid 267 or resid 269 through 270...
31(chain C and (resid 267 or resid 269 through 270...
41(chain D and (resid 267 or resid 269 through 270...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 267 or resid 269 through 270...A267
121(chain A and (resid 267 or resid 269 through 270...A269 - 270
131(chain A and (resid 267 or resid 269 through 270...A272 - 273
141(chain A and (resid 267 or resid 269 through 270...A2
151(chain A and (resid 267 or resid 269 through 270...A0
161(chain A and (resid 267 or resid 269 through 270...A323
171(chain A and (resid 267 or resid 269 through 270...A266 - 377
181(chain A and (resid 267 or resid 269 through 270...A266 - 377
191(chain A and (resid 267 or resid 269 through 270...A266 - 377
1101(chain A and (resid 267 or resid 269 through 270...A266 - 377
1111(chain A and (resid 267 or resid 269 through 270...A266 - 377
1121(chain A and (resid 267 or resid 269 through 270...A266 - 377
211(chain B and (resid 267 or resid 269 through 270...B267
221(chain B and (resid 267 or resid 269 through 270...B269 - 270
231(chain B and (resid 267 or resid 269 through 270...B272 - 273
241(chain B and (resid 267 or resid 269 through 270...B2
251(chain B and (resid 267 or resid 269 through 270...B0
261(chain B and (resid 267 or resid 269 through 270...B323
271(chain B and (resid 267 or resid 269 through 270...B263 - 378
281(chain B and (resid 267 or resid 269 through 270...B263 - 378
291(chain B and (resid 267 or resid 269 through 270...B263 - 378
2101(chain B and (resid 267 or resid 269 through 270...B263 - 378
2111(chain B and (resid 267 or resid 269 through 270...B263 - 378
2121(chain B and (resid 267 or resid 269 through 270...B263 - 378
311(chain C and (resid 267 or resid 269 through 270...C267
321(chain C and (resid 267 or resid 269 through 270...C269 - 270
331(chain C and (resid 267 or resid 269 through 270...C272 - 273
341(chain C and (resid 267 or resid 269 through 270...C267 - 378
351(chain C and (resid 267 or resid 269 through 270...C279 - 285
361(chain C and (resid 267 or resid 269 through 270...C288 - 313
371(chain C and (resid 267 or resid 269 through 270...C315 - 322
381(chain C and (resid 267 or resid 269 through 270...C323
391(chain C and (resid 267 or resid 269 through 270...C267 - 378
3101(chain C and (resid 267 or resid 269 through 270...C267 - 378
3111(chain C and (resid 267 or resid 269 through 270...C267 - 378
3121(chain C and (resid 267 or resid 269 through 270...C267 - 378
411(chain D and (resid 267 or resid 269 through 270...D267
421(chain D and (resid 267 or resid 269 through 270...D269 - 270
431(chain D and (resid 267 or resid 269 through 270...D272 - 273
441(chain D and (resid 267 or resid 269 through 270...D2
451(chain D and (resid 267 or resid 269 through 270...D0
461(chain D and (resid 267 or resid 269 through 270...D333 - 335
471(chain D and (resid 267 or resid 269 through 270...D265 - 378
481(chain D and (resid 267 or resid 269 through 270...D265 - 378
491(chain D and (resid 267 or resid 269 through 270...D265 - 378
4101(chain D and (resid 267 or resid 269 through 270...D265 - 378
4111(chain D and (resid 267 or resid 269 through 270...D265 - 378
4121(chain D and (resid 267 or resid 269 through 270...D265 - 378
4131(chain D and (resid 267 or resid 269 through 270...D265 - 378

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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-VYJ / 11-cyclopentyl-2-({2-ethoxy-4-[4-(4-methylpiperazin-1-yl)piperidine-1-carbonyl]phenyl}amino)-5-methyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one


Mass: 638.802 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C36H46N8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.87 Å3/Da / Density % sol: 57.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 3.5 M Sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.75→52.481 Å / Num. obs: 16151 / % possible obs: 99.6 % / Redundancy: 3.743 % / Biso Wilson estimate: 44.56 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.108 / Rrim(I) all: 0.127 / Χ2: 0.943 / Net I/σ(I): 10.62 / Num. measured all: 60455 / Scaling rejects: 13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.75-2.823.7590.5282.5611750.8150.617100
2.82-2.93.760.462.9211680.8450.53799.7
2.9-2.983.7620.413.3411410.8660.47999.4
2.98-3.073.7680.3284.1410740.9160.38399.6
3.07-3.183.7950.2824.7410560.9250.328100
3.18-3.293.7750.2116.2710130.9590.246100
3.29-3.413.7880.1687.8910150.9740.19699
3.41-3.553.7820.1399.49710.9820.16299.5
3.55-3.713.7560.10412.319040.9870.122100
3.71-3.893.7350.08514.038730.9920.099100
3.89-4.13.7430.08713.978370.9920.10299.6
4.1-4.353.690.06817.277990.9940.0899.5
4.35-4.653.6620.06517.937480.9950.07699.2
4.65-5.023.7670.06517.686900.9960.07699.9
5.02-5.53.7170.06617.476300.9940.077100
5.5-6.153.7610.07315.815860.9940.08599.7
6.15-7.13.730.06318.035080.9940.07499.8
7.1-8.73.7110.04424.044390.9970.05299.5
8.7-12.33.6390.03328.023410.9990.03899.4
12.3-52.4813.1260.03323.721830.9990.03993.4

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Processing

Software
NameVersionClassification
PHENIX1.19_4085refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VBQ

3vbq


Resolution: 2.75→52.48 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2643 808 5 %
Rwork0.2133 15337 -
obs0.2159 16145 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.4 Å2 / Biso mean: 49.9431 Å2 / Biso min: 13.58 Å2
Refinement stepCycle: final / Resolution: 2.75→52.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3748 0 193 56 3997
Biso mean--41.71 35.29 -
Num. residues----454
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1108X-RAY DIFFRACTION6.931TORSIONAL
12B1108X-RAY DIFFRACTION6.931TORSIONAL
13C1108X-RAY DIFFRACTION6.931TORSIONAL
14D1108X-RAY DIFFRACTION6.931TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.75-2.920.43041330.317125312664100
2.92-3.150.36671340.278125492683100
3.15-3.460.30311340.240725372671100
3.46-3.960.23961350.19625712706100
3.97-50.23571350.173325542689100
5-52.480.20831370.19272595273299
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)
16.4422-1.36370.2339.8007-1.56585.5242-0.1776-0.46650.13280.69230.34891.1258-1.1645-0.7165-0.16670.49040.02750.10360.3717-0.0730.5468-5.3771-3.239117.4213
25.4422-0.99340.02575.8939-0.06414.4096-0.3267-0.2922-1.15940.27070.1885-0.1253-0.05690.0805-0.15610.32110.0511-0.09010.307-0.02370.26116.2485-19.437616.0745
37.74162.92680.10815.8095-5.03835.7328-0.11621.8843-1.1987-0.85610.1295-1.3650.53370.71260.24620.222-0.03260.12950.6567-0.20280.692620.075-21.00243.7857
45.3586-1.7845-2.12565.55822.03983.2773-0.0615-0.43960.890.36220.3457-0.4372-0.27990.3652-0.53710.4266-0.0793-0.0310.2944-0.03720.43478.3419-6.25349.2206
55.3449-1.0106-2.21634.33541.70443.23390.0786-0.3122-0.0542-0.08730.01350.0216-0.13040.03980.06510.3546-0.0257-0.0420.2602-0.00130.2011-0.5317-15.71036.6628
67.4339-6.57585.15268.3909-6.68376.5685-0.3704-0.31380.09830.2570.60020.2779-0.1425-0.4027-0.02730.37710.00090.02590.4598-0.02460.2447-5.5284-20.835238.9309
76.9365-3.16890.54016.91680.80683.16910.3053-1.0899-0.40380.72760.21630.29480.6735-0.2198-0.42990.51620.0513-0.05160.37380.09380.26044.771-38.070244.6759
85.07963.5968-0.85395.9351-6.06818.955-0.56670.07770.21460.135-0.7678-2.1716-0.02262.271.25160.39750.0477-0.13290.51970.040.783423.4254-39.281443.5369
96.145-2.93391.68763.69290.18532.55160.124-0.23280.1020.2947-0.0657-0.37730.00880.0804-0.03520.3525-0.0281-0.03220.38920.0710.30786.978-30.655336.0036
104.3392-0.76260.0354.5204-0.17473.6359-0.1638-0.70150.01830.23250.3068-1.6233-0.1040.66010.01230.4074-0.076-0.13970.4667-0.00930.79236.3615-11.949215.7697
117.40323.3113-4.34836.07481.70635.4596-0.48462.29071.1685-2.1738-0.00421.3043-0.8344-1.28730.0680.44970.0371-0.2090.53990.09710.485816.0229-1.94774.1223
125.7395-1.880.76197.5113-2.36645.3207-0.01110.1429-0.4866-0.35410.0223-1.35830.12570.35110.02880.4876-0.11640.04380.3376-0.06860.649633.7218-10.8416.5875
132.22493.0189-1.95997.0616-1.35652.21220.1883-0.0701-0.6556-0.66810.0850.66940.3208-0.2513-0.33420.5576-0.1005-0.20220.45980.12510.61593.6183-42.464714.4336
143.61580.963-0.40935.032-1.90464.72640.1381-0.1435-0.6484-0.23740.27180.48820.656-0.2301-0.35470.3825-0.0239-0.13190.34060.10710.51097.3956-42.585420.7301
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 266 through 284 )A266 - 284
2X-RAY DIFFRACTION2chain 'A' and (resid 285 through 300 )A285 - 300
3X-RAY DIFFRACTION3chain 'A' and (resid 301 through 308 )A301 - 308
4X-RAY DIFFRACTION4chain 'A' and (resid 309 through 333 )A309 - 333
5X-RAY DIFFRACTION5chain 'A' and (resid 334 through 377 )A334 - 377
6X-RAY DIFFRACTION6chain 'B' and (resid 263 through 284 )B263 - 284
7X-RAY DIFFRACTION7chain 'B' and (resid 285 through 300 )B285 - 300
8X-RAY DIFFRACTION8chain 'B' and (resid 301 through 308 )B301 - 308
9X-RAY DIFFRACTION9chain 'B' and (resid 309 through 378 )B309 - 378
10X-RAY DIFFRACTION10chain 'C' and (resid 267 through 300 )C267 - 300
11X-RAY DIFFRACTION11chain 'C' and (resid 301 through 308 )C301 - 308
12X-RAY DIFFRACTION12chain 'C' and (resid 309 through 378 )C309 - 378
13X-RAY DIFFRACTION13chain 'D' and (resid 265 through 308 )D265 - 308
14X-RAY DIFFRACTION14chain 'D' and (resid 309 through 378 )D309 - 378

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