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- PDB-5dy7: Crystal structure of the human BRPF1 bromodomain in complex with SEED4 -

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Basic information

Entry
Database: PDB / ID: 5dy7
TitleCrystal structure of the human BRPF1 bromodomain in complex with SEED4
ComponentsPeregrin
KeywordsDNA BINDING PROTEIN / Bromodomain and PHD finger-containing protein 1(BRPF1) / monocytic leukemia zinc-finger (MOZ) / Inhibitor / transcription
Function / homology
Function and homology information


acetyltransferase activator activity / MOZ/MORF histone acetyltransferase complex / regulation of developmental process / regulation of hemopoiesis / histone acetyltransferase complex / Regulation of TP53 Activity through Acetylation / HATs acetylate histones / chromatin remodeling / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II ...acetyltransferase activator activity / MOZ/MORF histone acetyltransferase complex / regulation of developmental process / regulation of hemopoiesis / histone acetyltransferase complex / Regulation of TP53 Activity through Acetylation / HATs acetylate histones / chromatin remodeling / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / DNA binding / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
BRPF1, PHD domain / Peregrin, ePHD domain / : / : / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / PHD-finger / PHD-zinc-finger like domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. ...BRPF1, PHD domain / Peregrin, ePHD domain / : / : / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / PHD-finger / PHD-zinc-finger like domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Zinc finger, PHD-type, conserved site / Zinc finger C2H2 type domain profile. / Zinc finger PHD-type signature. / Zinc finger C2H2 type domain signature. / Zinc finger PHD-type profile. / Zinc finger C2H2-type / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Bromodomain-like / Histone Acetyltransferase; Chain A / Zinc finger, FYVE/PHD-type / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-5GT / NITRATE ION / Peregrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsZhu, J. / Caflisch, A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: J.Med.Chem. / Year: 2016
Title: Twenty Crystal Structures of Bromodomain and PHD Finger Containing Protein 1 (BRPF1)/Ligand Complexes Reveal Conserved Binding Motifs and Rare Interactions.
Authors: Zhu, J. / Caflisch, A.
History
DepositionSep 24, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peregrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9823
Polymers13,7041
Non-polymers2782
Water2,558142
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint1 kcal/mol
Surface area7040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.667, 60.667, 62.382
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-923-

HOH

21A-981-

HOH

31A-1024-

HOH

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Components

#1: Protein Peregrin / Bromodomain and PHD finger-containing protein 1 / Protein Br140


Mass: 13703.698 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRPF1, BR140 / Production host: Escherichia coli (E. coli) / References: UniProt: P55201
#2: Chemical ChemComp-5GT / 7-(trifluoromethyl)-3,4-dihydroquinoxalin-2(1H)-one


Mass: 216.160 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H7F3N2O
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M Sodium Acetate, pH5.5, 0.15 M Sodium Nitrate, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 1.69→40.19 Å / Num. obs: 15153 / % possible obs: 99.2 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.7
Reflection shellResolution: 1.69→1.78 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 4.5 / % possible all: 95.5

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LC2

4lc2


Resolution: 1.69→40.186 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2042 761 5.03 %
Rwork0.1797 --
obs0.181 15131 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.69→40.186 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms931 0 19 142 1092
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071010
X-RAY DIFFRACTIONf_angle_d0.7731369
X-RAY DIFFRACTIONf_dihedral_angle_d12.816635
X-RAY DIFFRACTIONf_chiral_restr0.045145
X-RAY DIFFRACTIONf_plane_restr0.005182
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6898-1.82020.30641520.24372725X-RAY DIFFRACTION96
1.8202-2.00340.21611470.20952854X-RAY DIFFRACTION100
2.0034-2.29330.23071320.1852893X-RAY DIFFRACTION100
2.2933-2.88920.24771730.19512885X-RAY DIFFRACTION100
2.8892-40.19690.1691570.16173013X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 27.0249 Å / Origin y: 1.7388 Å / Origin z: -9.91 Å
111213212223313233
T0.3513 Å20.0855 Å2-0.0162 Å2-0.1655 Å2-0.0089 Å2--0.1849 Å2
L5.6236 °20.0637 °21.3749 °2-1.6565 °20.1833 °2--1.6753 °2
S-0.2329 Å °-0.466 Å °-0.1387 Å °0.3195 Å °0.1427 Å °-0.0458 Å °-0.0844 Å °-0.1006 Å °0.0684 Å °
Refinement TLS groupSelection details: all

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