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- PDB-9fxp: Crystal structure of BRD4 BD1 with DI00626383. -

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Basic information

Entry
Database: PDB / ID: 9fxp
TitleCrystal structure of BRD4 BD1 with DI00626383.
ComponentsBromodomain-containing protein 4
KeywordsPROTEIN BINDING / Inhibitor / Bromodomain
Function / homologyAmanitin/phalloidin toxin / toxin activity / 4-methoxy-1,2-benzoxazol-3-amine / Alpha-amanitin proprotein 1
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsBader, G. / Reinert, D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2024
Title: Probing Protein-Ligand Methyl-pi Interaction Geometries through Chemical Shift Measurements of Selectively Labeled Methyl Groups.
Authors: Beier, A. / Platzer, G. / Hofurthner, T. / Ptaszek, A.L. / Lichtenecker, R.J. / Geist, L. / Fuchs, J.E. / McConnell, D.B. / Mayer, M. / Konrat, R.
History
DepositionJul 2, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2642
Polymers15,0991
Non-polymers1641
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.990, 43.980, 78.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Bromodomain-containing protein 4 / Protein HUNK1


Mass: 15099.380 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Production host: Escherichia coli (E. coli) / References: UniProt: O60885
#2: Chemical ChemComp-5WX / 4-methoxy-1,2-benzoxazol-3-amine


Mass: 164.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.11 Å3/Da / Density % sol: 41.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 16.5 % PEG 3350, 0.1 M sodium nitrate, 8 % ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.88→26.88 Å / Num. obs: 10493 / % possible obs: 96.4 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.036 / Rrim(I) all: 0.094 / Net I/σ(I): 19 / Num. measured all: 68160
Reflection shellResolution: 1.88→1.99 Å / % possible obs: 78.3 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.317 / Num. measured all: 5592 / Num. unique obs: 1222 / Rpim(I) all: 0.159 / Rrim(I) all: 0.356 / Net I/σ(I) obs: 5

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
SCALAdata scaling
XDSdata reduction
BUSTERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→26.88 Å / Cor.coef. Fo:Fc: 0.9368 / Cor.coef. Fo:Fc free: 0.9198 / SU R Cruickshank DPI: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.203 / SU Rfree Blow DPI: 0.157 / SU Rfree Cruickshank DPI: 0.146
RfactorNum. reflection% reflectionSelection details
Rfree0.2183 519 4.96 %RANDOM
Rwork0.1806 ---
obs0.1825 10455 96.01 %-
Displacement parametersBiso mean: 14.02 Å2
Baniso -1Baniso -2Baniso -3
1--1.7993 Å20 Å20 Å2
2--0.5077 Å20 Å2
3---1.2916 Å2
Refine analyzeLuzzati coordinate error obs: 0.218 Å
Refinement stepCycle: LAST / Resolution: 1.88→26.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1086 0 12 192 1290
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081130HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.911539HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d392SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes36HARMONIC2
X-RAY DIFFRACTIONt_gen_planes164HARMONIC5
X-RAY DIFFRACTIONt_it1130HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.29
X-RAY DIFFRACTIONt_other_torsion17.38
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion142SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies3HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1530SEMIHARMONIC4
LS refinement shellResolution: 1.88→2.1 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2276 133 5.1 %
Rwork0.2012 2473 -
all0.2026 2606 -
obs--96.01 %
Refinement TLS params.Method: refined / Origin x: 30.1875 Å / Origin y: 25.722 Å / Origin z: 8.9604 Å
111213212223313233
T-0.0286 Å2-0.0001 Å2-0.0031 Å2--0.0295 Å20.0117 Å2---0.0311 Å2
L0.4284 °20.1061 °20.2828 °2-0.6187 °20.0312 °2--0.7233 °2
S-0.0166 Å °0.0121 Å °0.0172 Å °0.0318 Å °0.0072 Å °-0.0135 Å °-0.0432 Å °-0.0213 Å °0.0095 Å °
Refinement TLS groupSelection details: { A|* }

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