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- PDB-6nim: Trypanosoma cruzi - BDF2, TcCLB.506553.20, solved with bromosporine -

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Basic information

Entry
Database: PDB / ID: 6nim
TitleTrypanosoma cruzi - BDF2, TcCLB.506553.20, solved with bromosporine
ComponentsBromodomain factor 2 protein
KeywordsSIGNALING PROTEIN / TcCLB.506553.20 / BDF2 / bromosporine / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Bromosporine / Bromodomain factor 2 protein
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.78 Å
AuthorsLin, Y.H. / Dong, A. / Tempel, W. / Loppnau, P. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Hui, R. / Vedadi, M. / Harding, R. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Trypanosoma cruzi - BDF2, TcCLB.506553.20, solved with bromosporine
Authors: Lin, Y.H. / Dong, A. / Tempel, W. / Loppnau, P. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Hui, R. / Vedadi, M. / Harding, R. / Structural Genomics Consortium (SGC)
History
DepositionDec 29, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Bromodomain factor 2 protein
B: Bromodomain factor 2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,02512
Polymers27,2372
Non-polymers78910
Water3,387188
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-42 kcal/mol
Surface area11870 Å2
Unit cell
Length a, b, c (Å)68.999, 65.784, 60.107
Angle α, β, γ (deg.)90.000, 110.640, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-206-

UNX

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Components

#1: Protein Bromodomain factor 2 protein


Mass: 13618.282 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: C4B63_57g96 / Plasmid: pET15-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-pRARE2 / References: UniProt: A0A2V2V5V1
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 5 / Source method: obtained synthetically
#4: Chemical ChemComp-BMF / Bromosporine / ethyl (3-methyl-6-{4-methyl-3-[(methylsulfonyl)amino]phenyl}[1,2,4]triazolo[4,3-b]pyridazin-8-yl)carbamate


Mass: 404.444 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20N6O4S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O

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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: 2.34 Å3/Da / Density % sol: 47.51 % / Mosaicity: 0.985 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 2.0 M NH4SO4 and 0.1M bis Tris pH5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Nov 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 23959 / % possible obs: 98.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.03 / Rrim(I) all: 0.061 / Χ2: 1.035 / Net I/σ(I): 11.3 / Num. measured all: 91630
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.78-1.812.90.45310120.820.2860.5390.89785.6
1.81-1.843.20.37211590.9120.230.440.8195.2
1.84-1.883.50.37411680.8850.2260.4390.81398.4
1.88-1.923.70.2912080.9210.1710.3380.84199.8
1.92-1.963.80.26411980.9410.1540.3070.87799.5
1.96-23.90.21312180.9450.1250.2480.88399.8
2-2.053.90.16911920.970.0980.1960.866100
2.05-2.113.90.14911920.980.0860.1720.95499.9
2.11-2.173.90.11912440.9820.0690.1380.896100
2.17-2.243.90.10111810.9890.0580.1170.952100
2.24-2.323.90.09512170.990.0550.110.992100
2.32-2.4240.08112110.9920.0470.0940.975100
2.42-2.5340.07412200.9930.0420.0851.043100
2.53-2.6640.06712180.9940.0390.0771.108100
2.66-2.8340.05611960.9960.0320.0651.081100
2.83-3.0440.04512100.9970.0260.0521.051100
3.04-3.3540.03812260.9980.0220.0441.071100
3.35-3.8340.03112220.9980.0180.0361.164100
3.83-4.8340.03112200.9990.0180.0361.355100
4.83-503.80.03712470.9980.0220.0431.84898.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.76 Å21.7 Å
Translation2.76 Å21.7 Å

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHASER2.8.2phasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CZG

5czg


Resolution: 1.78→21.71 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.561 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.112
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2044 935 4 %RANDOM
Rwork0.1703 ---
obs0.1717 22496 97.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 78.08 Å2 / Biso mean: 23.223 Å2 / Biso min: 14.41 Å2
Baniso -1Baniso -2Baniso -3
1--1.17 Å20 Å2-0.09 Å2
2--0.25 Å20 Å2
3---0.76 Å2
Refinement stepCycle: final / Resolution: 1.78→21.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1769 0 53 191 2013
Biso mean--42.38 34.13 -
Num. residues----226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131874
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171607
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.6282557
X-RAY DIFFRACTIONr_angle_other_deg1.4971.5823720
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7535228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.05223.654104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.52215284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.554158
X-RAY DIFFRACTIONr_chiral_restr0.0730.2234
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022161
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02390
LS refinement shellResolution: 1.782→1.828 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 53 -
Rwork0.302 1398 -
all-1451 -
obs--81.93 %

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