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- PDB-5c87: Crystal structure of the human BRPF1 bromodomain in complex with SEED2 -

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Basic information

Entry
Database: PDB / ID: 5c87
TitleCrystal structure of the human BRPF1 bromodomain in complex with SEED2
ComponentsPeregrin
KeywordsDNA BINDING PROTEIN / Bromodomain and PHD finger-containing protein 1(BRPF1) / monocytic leukemia zinc-finger (MOZ) / Inhibitor
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 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 / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
isoquinolin-1(2H)-one / NITRATE ION / Peregrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsZhu, J. / Caflisch, A.
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
DepositionJun 25, 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

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Assembly

Deposited unit
A: Peregrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9113
Polymers13,7041
Non-polymers2072
Water2,234124
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint0 kcal/mol
Surface area6940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.559, 60.559, 63.599
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-965-

HOH

21A-987-

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: 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-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-4YS / isoquinolin-1(2H)-one


Mass: 145.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H7NO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.46 Å3/Da / Density % sol: 49.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris propane, pH6.5, 0.2 M sodium nitrate, 20%PEG33500
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.55→30 Å / Num. obs: 20025 / % possible obs: 100 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 26.6
Reflection shellResolution: 1.55→1.63 Å / Redundancy: 6 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 4.8 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LC2

4lc2


Resolution: 1.55→27.339 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1984 997 4.98 %
Rwork0.1818 --
obs0.1827 20001 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→27.339 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms927 0 15 124 1066
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007992
X-RAY DIFFRACTIONf_angle_d0.921340
X-RAY DIFFRACTIONf_dihedral_angle_d11.947385
X-RAY DIFFRACTIONf_chiral_restr0.04142
X-RAY DIFFRACTIONf_plane_restr0.004177
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5502-1.6320.26411330.22122668X-RAY DIFFRACTION100
1.632-1.73420.25681640.21252652X-RAY DIFFRACTION100
1.7342-1.86810.22321340.20162688X-RAY DIFFRACTION100
1.8681-2.0560.21171480.20682689X-RAY DIFFRACTION100
2.056-2.35340.20391380.1872717X-RAY DIFFRACTION100
2.3534-2.96440.19031340.20262735X-RAY DIFFRACTION100
2.9644-27.34340.18711460.16112855X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 14.9947 Å / Origin y: -23.0031 Å / Origin z: 0.3542 Å
111213212223313233
T0.2278 Å2-0.0967 Å2-0.0273 Å2-0.2096 Å20.0121 Å2--0.1582 Å2
L2.987 °2-0.3997 °21.2945 °2-4.5465 °2-1.2166 °2--2.5861 °2
S0.0616 Å °-0.309 Å °-0.112 Å °0.5294 Å °-0.1651 Å °0.0686 Å °-0.007 Å °-0.1112 Å °0.0529 Å °
Refinement TLS groupSelection details: all

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