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- PDB-5dfb: Crystal structure of BRD2(BD2) mutant W370F in the free form -

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Basic information

Entry
Database: PDB / ID: 5dfb
TitleCrystal structure of BRD2(BD2) mutant W370F in the free form
ComponentsBromodomain-containing protein 2
KeywordsTRANSCRIPTION / Transcription factors / BET bromodomains / protein mutation engineering / molecular probes
Function / homology
Function and homology information


histone H4K12ac reader activity / histone H4K5ac reader activity / histone H3K14ac reader activity / acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / nucleosome assembly ...histone H4K12ac reader activity / histone H4K5ac reader activity / histone H3K14ac reader activity / acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / nucleosome assembly / spermatogenesis / histone binding / nuclear speck / chromatin remodeling / protein serine/threonine kinase activity / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site ...Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
NICKEL (II) ION / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsTallant, C. / Baud, M. / Lin-Shiao, E. / Chirgadze, D.Y. / Ciulli, A.
CitationJournal: J.Med.Chem. / Year: 2016
Title: New Synthetic Routes to Triazolo-benzodiazepine Analogues: Expanding the Scope of the Bump-and-Hole Approach for Selective Bromo and Extra-Terminal (BET) Bromodomain Inhibition.
Authors: Baud, M.G. / Lin-Shiao, E. / Zengerle, M. / Tallant, C. / Ciulli, A.
History
DepositionAug 26, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 9, 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: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9024
Polymers13,3361
Non-polymers5653
Water1,36976
1
A: Bromodomain-containing protein 2
hetero molecules

A: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8038
Polymers26,6732
Non-polymers1,1316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545x,-y-1,-z1
Buried area2540 Å2
ΔGint-25 kcal/mol
Surface area12580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.118, 52.731, 71.464
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-501-

NI

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Components

#1: Protein Bromodomain-containing protein 2 / O27.1.1 / Really interesting new gene 3 protein


Mass: 13336.374 Da / Num. of mol.: 1 / Fragment: UNP Residues 344-455 / Mutation: W370F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2, KIAA9001, RING3 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P25440
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.27 Å3/Da / Density % sol: 45.92 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M Hepes pH 7, 0.2M Imidiazole, 41% PEG 400 / PH range: 7

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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: Oct 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.4→29.58 Å / Num. all: 24545 / Num. obs: 24545 / % possible obs: 99.6 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.035 / Rsym value: 0.015 / Net I/av σ(I): 16.5 / Net I/σ(I): 34.1
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.091 / Mean I/σ(I) obs: 16.5 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DVV

2dvv


Resolution: 1.4→29.58 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.224 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16923 1250 5.1 %RANDOM
Rwork0.15688 ---
obs0.15755 23252 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.809 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2---0.07 Å20 Å2
3----0.04 Å2
Refinement stepCycle: 1 / Resolution: 1.4→29.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms891 0 29 76 996
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.019947
X-RAY DIFFRACTIONr_bond_other_d0.0010.02905
X-RAY DIFFRACTIONr_angle_refined_deg1.5071.9761266
X-RAY DIFFRACTIONr_angle_other_deg0.80832094
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5845109
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.92523.54248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.84315165
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.249156
X-RAY DIFFRACTIONr_chiral_restr0.0950.2127
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211032
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02222
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.158 83 -
Rwork0.155 1659 -
obs--98.86 %
Refinement TLS params.Method: refined / Details: Chain A / Origin x: -15.1028 Å / Origin y: -15.9909 Å / Origin z: 2.5246 Å
111213212223313233
T0.0125 Å2-0.0049 Å2-0.001 Å2-0.0145 Å2-0.0028 Å2--0.0013 Å2
L0.0128 °20.0543 °2-0.0447 °2-0.36 °20.037 °2--0.6767 °2
S-0.0013 Å °-0.002 Å °-0.0005 Å °-0.0145 Å °0.004 Å °-0.0097 Å °-0.0055 Å °-0.011 Å °-0.0027 Å °

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