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- PDB-7uge: Bromodomain of CBP liganded with BMS-536924 -

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Basic information

Entry
Database: PDB / ID: 7uge
TitleBromodomain of CBP liganded with BMS-536924
ComponentsHistone acetyltransferase
KeywordsTRANSCRIPTION / bromodomain / small molecule ligand / complex
Function / homology
Function and homology information


histone acetyltransferase activity / histone acetyltransferase / transcription coregulator activity / nuclear body / regulation of DNA-templated transcription / nucleoplasm
Similarity search - Function
: / Histone acetyltransferase p300-like, PHD domain / Coactivator CBP, KIX domain / CREB-binding protein/p300, atypical RING domain / CBP/p300-type histone acetyltransferase domain / CBP/p300, atypical RING domain superfamily / KIX domain / CREB-binding protein/p300, atypical RING domain / KIX domain profile. / CBP/p300-type histone acetyltransferase (HAT) domain profile. ...: / Histone acetyltransferase p300-like, PHD domain / Coactivator CBP, KIX domain / CREB-binding protein/p300, atypical RING domain / CBP/p300-type histone acetyltransferase domain / CBP/p300, atypical RING domain superfamily / KIX domain / CREB-binding protein/p300, atypical RING domain / KIX domain profile. / CBP/p300-type histone acetyltransferase (HAT) domain profile. / Histone acetyltransferase Rtt109/CBP / Histone acetylation protein / Histone acetylation protein / Coactivator CBP, KIX domain superfamily / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Chem-N6I / histone acetyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.004 Å
AuthorsSchonbrunn, E. / Bikowitz, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structural basis of CBP and EP300 interaction with kinase inhibitors
Authors: Schonbrunn, E. / Bikowitz, M.
History
DepositionMar 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 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: Histone acetyltransferase
B: Histone acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7185
Polymers27,6962
Non-polymers1,0223
Water3,891216
1
A: Histone acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3282
Polymers13,8481
Non-polymers4801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Histone acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3903
Polymers13,8481
Non-polymers5422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.122, 59.293, 57.147
Angle α, β, γ (deg.)90.000, 109.810, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Histone acetyltransferase


Mass: 13847.882 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CREBBP / Production host: Escherichia coli (E. coli) / References: UniProt: I3L466, histone acetyltransferase
#2: Chemical ChemComp-N6I / (3M)-4-{[(2S)-2-(3-chlorophenyl)-2-hydroxyethyl]amino}-3-[4-methyl-6-(morpholin-4-yl)-1H-benzimidazol-2-yl]pyridin-2(1H)-one


Mass: 479.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H26ClN5O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.48 Å3/Da / Density % sol: 50.44 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 0.2M Lithium sulfate monohydrate, 0.1M BIS-TRIS pH6.5, 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2→39.83 Å / Num. obs: 17935 / % possible obs: 97.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 18.7 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.121 / Net I/σ(I): 16.1
Reflection shellResolution: 2→2.03 Å / Mean I/σ(I) obs: 3.3 / Num. unique obs: 894 / CC1/2: 0.889 / Rrim(I) all: 0.382

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7KPY

7kpy


Resolution: 2.004→39.829 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1971 1082 6.04 %
Rwork0.1644 16833 -
obs0.1665 17915 97.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.73 Å2 / Biso mean: 21.6623 Å2 / Biso min: 11.57 Å2
Refinement stepCycle: final / Resolution: 2.004→39.829 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1950 0 72 216 2238
Biso mean--18.24 28.03 -
Num. residues----232
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.004-2.09470.23751260.1791201494
2.0947-2.20520.21281320.1671206097
2.2052-2.34330.2121380.1663209197
2.3433-2.52420.22871360.1685208897
2.5242-2.77820.20281270.1773210098
2.7782-3.18010.21581400.1779214699
3.1801-4.00590.19011430.1529213499
4.0059-39.8290.15721400.154220099
Refinement TLS params.Method: refined / Origin x: 14.6585 Å / Origin y: 8.9858 Å / Origin z: -20.8517 Å
111213212223313233
T0.1488 Å2-0.0114 Å2-0.0094 Å2-0.1353 Å2-0.007 Å2--0.1566 Å2
L0.9821 °2-0.071 °2-0.2864 °2-0.3711 °20.099 °2--0.4838 °2
S0.0472 Å °-0.0175 Å °0.0173 Å °0.01 Å °-0.0102 Å °0.0028 Å °-0.0141 Å °0.0223 Å °-0.0346 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1082 - 1197
2X-RAY DIFFRACTION1allB1082 - 1197
3X-RAY DIFFRACTION1allI1 - 2
4X-RAY DIFFRACTION1allE1
5X-RAY DIFFRACTION1allQ1 - 219

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