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- PDB-5ev9: Crystal structure of the human BRPF1 bromodomain in complex with ... -

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Basic information

Entry
Database: PDB / ID: 5ev9
TitleCrystal structure of the human BRPF1 bromodomain in complex with SEED15
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
Chem-5SB / NITRATE ION / Peregrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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 19, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 8, 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

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Assembly

Deposited unit
A: Peregrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0183
Polymers13,7041
Non-polymers3142
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint2 kcal/mol
Surface area6870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.360, 60.360, 63.460
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-976-

HOH

21A-992-

HOH

31A-999-

HOH

41A-1012-

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 626-740
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-5SB / ~{N}-[5-(1~{H}-pyrazol-4-yl)quinolin-8-yl]ethanamide


Mass: 252.271 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H12N4O
#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.: 126 / Source method: isolated from a natural source / Formula: H2O

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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: 2.51 Å3/Da / Density % sol: 50.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
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: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→40.35 Å / Num. obs: 24170 / % possible obs: 100 % / Redundancy: 9.4 % / Rsym value: 0.032 / Net I/σ(I): 33
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.285 / % possible all: 99.9

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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: 1.45→40.348 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2207 1207 5 %
Rwork0.1886 --
obs0.1902 24144 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→40.348 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms922 0 23 126 1071
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009984
X-RAY DIFFRACTIONf_angle_d0.8851330
X-RAY DIFFRACTIONf_dihedral_angle_d16.708382
X-RAY DIFFRACTIONf_chiral_restr0.068141
X-RAY DIFFRACTIONf_plane_restr0.005175
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4503-1.50830.25771340.24252539X-RAY DIFFRACTION100
1.5083-1.5770.24261310.21932486X-RAY DIFFRACTION100
1.577-1.66010.29011320.22552519X-RAY DIFFRACTION100
1.6601-1.76410.27131310.21952506X-RAY DIFFRACTION100
1.7641-1.90030.24841340.21072548X-RAY DIFFRACTION100
1.9003-2.09160.23181340.20212532X-RAY DIFFRACTION100
2.0916-2.39420.21551330.18982549X-RAY DIFFRACTION100
2.3942-3.01630.22711360.19682585X-RAY DIFFRACTION100
3.0163-40.36320.20371420.17222673X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -14.8496 Å / Origin y: 22.5067 Å / Origin z: 63.8327 Å
111213212223313233
T0.23 Å2-0.1072 Å20.0499 Å2-0.2454 Å2-0.0055 Å2--0.1699 Å2
L2.0913 °2-0.2027 °2-0.8192 °2-5.6557 °21.4594 °2--2.9987 °2
S0.0787 Å °-0.259 Å °0.0402 Å °0.5288 Å °-0.2862 Å °0.0326 Å °0.0612 Å °0.0804 Å °-0.164 Å °
Refinement TLS groupSelection details: all

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