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- PDB-7laj: Crystal structure of the first bromodomain (BD1) of human BRD2 bo... -

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Basic information

Entry
Database: PDB / ID: 7laj
TitleCrystal structure of the first bromodomain (BD1) of human BRD2 bound to Ro3280
ComponentsBromodomain-containing protein 2
KeywordsGENE REGULATION / BET / ERK5 / dual BRD-kinase inhibitor
Function / homology
Function and homology information


chromatin organization / chromosome / nuclear speck / nucleoplasm
Similarity search - Function
Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / : / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain (BrD) profile. / bromo domain / Bromodomain / Bromodomain-like superfamily
Similarity search - Domain/homology
Chem-79C / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.854 Å
AuthorsKarim, M.R. / Bikowitz, M. / Chan, A. / 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 6, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 17, 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0152
Polymers14,4721
Non-polymers5441
Water1,892105
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.920, 82.670, 45.200
Angle α, β, γ (deg.)90.000, 134.330, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-318-

HOH

21A-337-

HOH

31A-392-

HOH

41A-393-

HOH

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Components

#1: Protein Bromodomain-containing protein 2


Mass: 14471.866 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2 / Production host: Escherichia coli (E. coli) / References: UniProt: U3KQA6
#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.: 1 / Source method: obtained synthetically / Formula: C27H35F2N7O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.49 Å3/Da / Density % sol: 50.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 60 % v/v Tacsimate pH 7.0

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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: Feb 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→39.091 Å / Num. obs: 11663 / % possible obs: 95.5 % / Redundancy: 3.574 % / Biso Wilson estimate: 23.97 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.028 / Rrim(I) all: 0.033 / Χ2: 1.007 / Net I/σ(I): 28.12 / Num. measured all: 41685 / Scaling rejects: 2
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
1.85-1.91.9940.1535.2513889006960.9690.19577.3
1.9-1.953.3090.1399.0227668818360.9830.16694.9
1.95-2.013.6690.10811.9229358368000.9930.12695.7
2.01-2.073.680.07615.5330218548210.9960.08996.1
2.07-2.143.7070.05619.3327887757520.9980.06697
2.14-2.223.7190.04722.7627417607370.9980.05697
2.22-2.33.7310.04324.3627357597330.9980.05196.6
2.3-2.393.7170.03927.2526247287060.9980.04697
2.39-2.53.6990.03628.6325046926770.9980.04397.8
2.5-2.623.7410.03532.1124586716570.9980.0497.9
2.62-2.763.710.03135.2422636256100.9980.03697.6
2.76-2.933.7170.02837.5121715935840.9990.03398.5
2.93-3.133.7650.02740.1420825655530.9990.03197.9
3.13-3.393.6660.02443.7518445115030.9990.02898.4
3.39-3.713.7230.02347.3717464794690.9990.02797.9
3.71-4.153.6810.02248.9216384584450.9990.02697.2
4.15-4.793.7470.02150.2313943783720.9990.02598.4
4.79-5.863.7060.02249.212083353260.9990.02697.3
5.86-8.293.660.02149.479152622500.9990.02595.4
8.29-39.0913.4120.0250.74641491360.9990.02491.3

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
PROTEUM PLUSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7LAH

7lah


Resolution: 1.854→39.091 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 24.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2119 584 5.01 %
Rwork0.164 11078 -
obs0.1664 11662 96.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.6 Å2 / Biso mean: 29.1592 Å2 / Biso min: 12.69 Å2
Refinement stepCycle: final / Resolution: 1.854→39.091 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1014 0 39 105 1158
Biso mean--33.61 37.59 -
Num. residues----122
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8541-2.04070.2551370.1982259391
2.0407-2.33590.25341470.1729278898
2.3359-2.94290.22931480.1775282699
2.9429-39.090.18121520.1486287199
Refinement TLS params.Method: refined / Origin x: -16.1784 Å / Origin y: -16.8901 Å / Origin z: 1.111 Å
111213212223313233
T0.1352 Å2-0.0108 Å20.024 Å2-0.1761 Å2-0.0138 Å2--0.1501 Å2
L1.2637 °2-0.3052 °20.0814 °2-5.1223 °2-1.2765 °2--1.0943 °2
S-0.0311 Å °-0.0247 Å °0.018 Å °0.0603 Å °-0.003 Å °-0.129 Å °-0.0249 Å °0.0717 Å °0.0385 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA73 - 194
2X-RAY DIFFRACTION1allI1
3X-RAY DIFFRACTION1allQ1 - 105

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