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- PDB-5fg6: Crystal structure of the bromodomain of human BRD1 (BRPF2) in com... -

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Basic information

Entry
Database: PDB / ID: 5fg6
TitleCrystal structure of the bromodomain of human BRD1 (BRPF2) in complex with OF-1 chemical probe
ComponentsBromodomain-containing protein 1
KeywordsTRANSCRIPTION / MOZ-MORF complex
Function / homology
Function and homology information


histone H3-K14 acetyltransferase complex / MOZ/MORF histone acetyltransferase complex / regulation of developmental process / regulation of hemopoiesis / erythrocyte maturation / response to immobilization stress / response to electrical stimulus / Regulation of TP53 Activity through Acetylation / histone reader activity / positive regulation of erythrocyte differentiation ...histone H3-K14 acetyltransferase complex / MOZ/MORF histone acetyltransferase complex / regulation of developmental process / regulation of hemopoiesis / erythrocyte maturation / response to immobilization stress / response to electrical stimulus / Regulation of TP53 Activity through Acetylation / histone reader activity / positive regulation of erythrocyte differentiation / HATs acetylate histones / histone binding / perikaryon / nuclear speck / chromatin remodeling / dendrite / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / nucleus / metal ion binding
Similarity search - Function
BRPF2, ePHD domain / BRPF2, PHD 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 ...BRPF2, ePHD domain / BRPF2, PHD 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 PHD-type signature. / 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-5XE / NICKEL (II) ION / PHOSPHATE ION / Bromodomain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsTallant, C. / Owen, D.R. / Gerstenberger, B.S. / Savitsky, P. / Chaikuad, A. / Fedorov, O. / Nunez-Alonso, G. / Filippakopoulos, P. / von Delft, F. / Arrowsmith, C.H. ...Tallant, C. / Owen, D.R. / Gerstenberger, B.S. / Savitsky, P. / Chaikuad, A. / Fedorov, O. / Nunez-Alonso, G. / Filippakopoulos, P. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Muller, S. / Knapp, S.
CitationJournal: To Be Published
Title: Crystal structure of the bromodomain of human BRD1 (BRPF2) in complex with OF-1 chemical probe
Authors: Tallant, C. / Owen, D.R. / Gerstenberger, B.S. / Savitsky, P. / Chaikuad, A. / Fedorov, O. / Nunez-Alonso, G. / Filippakopoulos, P. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / ...Authors: Tallant, C. / Owen, D.R. / Gerstenberger, B.S. / Savitsky, P. / Chaikuad, A. / Fedorov, O. / Nunez-Alonso, G. / Filippakopoulos, P. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Muller, S. / Knapp, S.
History
DepositionDec 20, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
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

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Assembly

Deposited unit
A: Bromodomain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7048
Polymers14,8621
Non-polymers8427
Water3,423190
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-1 kcal/mol
Surface area7780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.771, 84.328, 52.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-706-

NI

21A-804-

HOH

31A-960-

HOH

41A-988-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Bromodomain-containing protein 1 / BR140-like protein / Bromodomain and PHD finger-containing protein 2


Mass: 14862.024 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD1, BRL, BRPF2 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / References: UniProt: O95696

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Non-polymers , 5 types, 197 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-5XE / 4-bromanyl-~{N}-(6-methoxy-1,3-dimethyl-2-oxidanylidene-benzimidazol-5-yl)-2-methyl-benzenesulfonamide


Mass: 440.312 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H18BrN3O4S
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.62 Å3/Da / Density % sol: 53.05 % / Description: Rod
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M tri-sodium citrate dihydrate pH 5.6, 1 M ammoinum dihydrogen phosphate
PH range: 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.1→29.27 Å / Num. all: 62094 / Num. obs: 62094 / % possible obs: 97.9 % / Redundancy: 9.1 % / Biso Wilson estimate: 8.788 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.034 / Net I/σ(I): 22
Reflection shellResolution: 1.1→1.12 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.168 / Mean I/σ(I) obs: 6.4 / % possible all: 79.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RCW

3rcw


Resolution: 1.1→29.27 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 0.353 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.031 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19671 3069 4.9 %RANDOM
Rwork0.18096 ---
obs0.18173 59008 97.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.513 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0 Å20 Å2
2---0.07 Å2-0 Å2
3---0.32 Å2
Refinement stepCycle: 1 / Resolution: 1.1→29.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms962 0 48 190 1200
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191055
X-RAY DIFFRACTIONr_bond_other_d0.0020.021026
X-RAY DIFFRACTIONr_angle_refined_deg1.4612.0161423
X-RAY DIFFRACTIONr_angle_other_deg0.953.0052342
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9615123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.31622.67956
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.01915187
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5951514
X-RAY DIFFRACTIONr_chiral_restr0.0790.2149
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211180
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02254
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6410.994483
X-RAY DIFFRACTIONr_mcbond_other0.620.989482
X-RAY DIFFRACTIONr_mcangle_it0.9821.49606
X-RAY DIFFRACTIONr_mcangle_other0.9831.494607
X-RAY DIFFRACTIONr_scbond_it1.1981.213572
X-RAY DIFFRACTIONr_scbond_other1.1991.205569
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9381.71811
X-RAY DIFFRACTIONr_long_range_B_refined4.9059.7081463
X-RAY DIFFRACTIONr_long_range_B_other4.4088.7811348
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.099→1.128 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.196 190 -
Rwork0.192 3518 -
obs--79.83 %

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