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- PDB-7c4i: High resolution structure of BRPF1 Bromo Domain from Biortus -

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Basic information

Entry
Database: PDB / ID: 7c4i
TitleHigh resolution structure of BRPF1 Bromo Domain from Biortus
ComponentsPeregrin
KeywordsDNA BINDING PROTEIN
Function / homology
Function and homology information


acetyltransferase activator activity / regulation of developmental process / MOZ/MORF histone acetyltransferase complex / 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 / regulation of developmental process / MOZ/MORF histone acetyltransferase complex / 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 / metal ion binding / nucleus / 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. / domain with conserved PWWP motif ...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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsWang, F. / Lin, D. / Lv, Z. / Zhu, B.
CitationJournal: To Be Published
Title: High resolution structure of BRPF1 Bromo Domain from Biortus
Authors: Wang, F. / Lin, D. / Lv, Z. / Zhu, B.
History
DepositionMay 18, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Derived calculations / Structure summary
Category: citation / database_2 ...citation / database_2 / struct / struct_conn
Item: _citation.title / _database_2.pdbx_DOI ..._citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct.title / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.2Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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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)16,33911
Polymers15,6301
Non-polymers70910
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-1 kcal/mol
Surface area7470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.601, 60.601, 59.169
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-400-

HOH

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Components

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


Mass: 15629.786 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-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.01 Å3/Da / Density % sol: 38.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Potassium fluoride, 20 %(w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97936 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97936 Å / Relative weight: 1
ReflectionResolution: 1.37→39.293 Å / Num. obs: 26865 / % possible obs: 100 % / Redundancy: 7.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Net I/σ(I): 12.3
Reflection shellResolution: 1.37→1.39 Å / Num. unique obs: 1349 / CC1/2: 0.797

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ewc

5ewc


Resolution: 1.37→39.293 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / WRfactor Rfree: 0.203 / WRfactor Rwork: 0.174 / SU B: 1.094 / SU ML: 0.043 / Average fsc free: 0.9254 / Average fsc work: 0.9304 / Cross valid method: FREE R-VALUE / ESU R: 0.057 / ESU R Free: 0.059
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1937 1367 5.095 %
Rwork0.1663 25465 -
all0.168 --
obs-26832 99.944 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 20.364 Å2
Baniso -1Baniso -2Baniso -3
1--0.552 Å2-0.276 Å20 Å2
2---0.552 Å20 Å2
3---1.792 Å2
Refinement stepCycle: LAST / Resolution: 1.37→39.293 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms960 0 40 151 1151
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0131093
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171028
X-RAY DIFFRACTIONr_angle_refined_deg1.3561.661470
X-RAY DIFFRACTIONr_angle_other_deg1.4121.5832394
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8815132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.2521.83171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.01915205
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4081511
X-RAY DIFFRACTIONr_chiral_restr0.0720.2131
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021231
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02242
X-RAY DIFFRACTIONr_nbd_refined0.2740.2265
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2060.2869
X-RAY DIFFRACTIONr_nbtor_refined0.1720.2520
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.2372
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.294
X-RAY DIFFRACTIONr_metal_ion_refined0.1830.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1960.219
X-RAY DIFFRACTIONr_nbd_other0.2360.247
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.130.216
X-RAY DIFFRACTIONr_mcbond_it1.031.764501
X-RAY DIFFRACTIONr_mcbond_other1.0281.761499
X-RAY DIFFRACTIONr_mcangle_it1.4842.642636
X-RAY DIFFRACTIONr_mcangle_other1.4852.642636
X-RAY DIFFRACTIONr_scbond_it2.1362.261592
X-RAY DIFFRACTIONr_scbond_other2.1342.263593
X-RAY DIFFRACTIONr_scangle_it3.3473.231832
X-RAY DIFFRACTIONr_scangle_other3.3453.234833
X-RAY DIFFRACTIONr_lrange_it5.89623.5291328
X-RAY DIFFRACTIONr_lrange_other5.75122.8961295
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.4060.271080.2461846X-RAY DIFFRACTION100
1.406-1.4440.226790.231831X-RAY DIFFRACTION100
1.444-1.4860.238840.221786X-RAY DIFFRACTION100
1.486-1.5320.226960.1981687X-RAY DIFFRACTION99.888
1.532-1.5820.195940.1871671X-RAY DIFFRACTION100
1.582-1.6370.186920.1771592X-RAY DIFFRACTION100
1.637-1.6990.223780.1731554X-RAY DIFFRACTION100
1.699-1.7680.182820.1671490X-RAY DIFFRACTION100
1.768-1.8470.201730.1581464X-RAY DIFFRACTION100
1.847-1.9370.168610.1631377X-RAY DIFFRACTION99.9305
1.937-2.0420.202800.1631316X-RAY DIFFRACTION100
2.042-2.1650.179860.1591235X-RAY DIFFRACTION100
2.165-2.3140.182660.1561147X-RAY DIFFRACTION99.9176
2.314-2.4990.198520.1561121X-RAY DIFFRACTION100
2.499-2.7370.209640.1591005X-RAY DIFFRACTION100
2.737-3.0590.206540.162912X-RAY DIFFRACTION99.8966
3.059-3.5310.188410.153829X-RAY DIFFRACTION100
3.531-4.3190.129330.146706X-RAY DIFFRACTION99.8649
4.319-6.0880.204300.174561X-RAY DIFFRACTION99.6627
6.088-39.2930.282140.19335X-RAY DIFFRACTION99.1477

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