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- PDB-5eps: Crystal structure of the human BRPF1 bromodomain in complex with ... -

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Basic information

Entry
Database: PDB / ID: 5eps
TitleCrystal structure of the human BRPF1 bromodomain in complex with SEED10
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 / nucleoplasm / nucleus / metal ion binding / plasma membrane / cytosol / cytoplasm
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 C2H2 type domain profile. / Zinc finger, PHD-type, conserved site / Zinc finger C2H2 type domain signature. / Zinc finger PHD-type signature. / Zinc finger C2H2-type / Zinc finger PHD-type profile. / 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 / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
1-methyl-3,4-dihydroquinoxalin-2-one / NITRATE ION / Peregrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 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
DepositionNov 12, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 2.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _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)13,9283
Polymers13,7041
Non-polymers2242
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint1 kcal/mol
Surface area7090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.630, 60.630, 62.500
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-909-

HOH

21A-972-

HOH

31A-997-

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 / Fragment: UNP residues 625-740
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-5QX / 1-methyl-3,4-dihydroquinoxalin-2-one


Mass: 162.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10N2O
#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.: 111 / 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: 49.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M 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: PSI 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: 1.47→40.2 Å / Num. obs: 23061 / % possible obs: 100 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 25.4
Reflection shellResolution: 1.47→1.55 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.285 / Mean I/σ(I) obs: 6.6 / % possible all: 99.8

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Processing

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

4lc2


Resolution: 1.47→40.2 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1981 1152 5 %
Rwork0.1884 --
obs0.1889 23034 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.47→40.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms934 0 16 111 1061
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007998
X-RAY DIFFRACTIONf_angle_d0.7381350
X-RAY DIFFRACTIONf_dihedral_angle_d15.307398
X-RAY DIFFRACTIONf_chiral_restr0.068143
X-RAY DIFFRACTIONf_plane_restr0.005180
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4701-1.5370.25051400.20282671X-RAY DIFFRACTION100
1.537-1.6180.22781420.19642703X-RAY DIFFRACTION100
1.618-1.71940.22081430.19852703X-RAY DIFFRACTION100
1.7194-1.85210.22281440.20162732X-RAY DIFFRACTION100
1.8521-2.03850.2431420.20952692X-RAY DIFFRACTION100
2.0385-2.33350.20211440.18892752X-RAY DIFFRACTION100
2.3335-2.93980.19691450.20092743X-RAY DIFFRACTION100
2.9398-40.21770.18051520.17552886X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 27.2746 Å / Origin y: 1.6725 Å / Origin z: -9.9333 Å
111213212223313233
T0.3286 Å20.0927 Å2-0.0216 Å2-0.1605 Å2-0.0174 Å2--0.2005 Å2
L5.0516 °2-0.321 °21.3897 °2-1.0942 °2-0.0107 °2--1.438 °2
S-0.2975 Å °-0.4204 Å °-0.1387 Å °0.2028 Å °0.1947 Å °-0.0705 Å °-0.0959 Å °-0.098 Å °0.081 Å °
Refinement TLS groupSelection details: all

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