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- PDB-6np7: Crystal structure of Trypanosoma cruzi bromodomain BDF2 (TcCLB.50... -

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Basic information

Entry
Database: PDB / ID: 6np7
TitleCrystal structure of Trypanosoma cruzi bromodomain BDF2 (TcCLB.506553.20)
ComponentsBromodomain factor 2 protein
KeywordsTRANSCRIPTION / bromodomain BDF2 and TcCLB.506553.20 / 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 ...: / 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
Bromodomain factor 2 protein
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / Resolution: 2.16 Å
AuthorsLin, Y.H. / Dong, A. / Loppnau, P. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Vedadi, M. / Hui, R. / Harding, R.J. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal structure of Trypanosoma cruzi bromodomain BDF2 (TcCLB.506553.20)
Authors: Lin, Y.H. / Dong, A. / Loppnau, P. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Vedadi, M. / Hui, R. / Harding, R.J. / Structural Genomics Consortium (SGC)
History
DepositionJan 17, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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 factor 2 protein
B: Bromodomain factor 2 protein


Theoretical massNumber of molelcules
Total (without water)27,2372
Polymers27,2372
Non-polymers00
Water82946
1
A: Bromodomain factor 2 protein


Theoretical massNumber of molelcules
Total (without water)13,6181
Polymers13,6181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain factor 2 protein


Theoretical massNumber of molelcules
Total (without water)13,6181
Polymers13,6181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.317, 66.085, 60.580
Angle α, β, γ (deg.)90.000, 110.890, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Bromodomain factor 2 protein


Mass: 13618.282 Da / Num. of mol.: 2 / Fragment: UNP Residues 1-120
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.38 Å3/Da / Density % sol: 48.31 % / Mosaicity: 4.06 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1.4M NaCitrate, and 0.1M HEPES pH7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Jan 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.16→50 Å / Num. obs: 13243 / % possible obs: 94.7 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.069 / Rrim(I) all: 0.118 / Χ2: 2.28 / Net I/σ(I): 10.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.16-2.21.80.4385230.7110.3390.5581.45874.8
2.2-2.241.90.3585690.7850.2760.4551.46181.8
2.24-2.282.10.3686140.8120.2790.4641.4289.2
2.28-2.332.20.426460.7680.3270.5351.41192.3
2.33-2.382.40.3556570.8740.2690.4481.3595.8
2.38-2.432.50.336750.860.2390.4091.28797.4
2.43-2.492.50.3066850.8910.2250.3821.43297.4
2.49-2.562.60.2666790.9030.1910.331.38596.7
2.56-2.642.60.2466690.920.1750.3031.51597.7
2.64-2.722.60.2156790.9220.1570.2681.62598.1
2.72-2.822.60.1916870.9430.1380.2371.8797.6
2.82-2.932.60.1646810.9540.1180.2032.15997.7
2.93-3.062.60.1296640.9690.0920.1592.03196.7
3.06-3.232.60.1197010.9710.0860.1482.51297.1
3.23-3.432.60.0976630.9820.0710.1212.81496.4
3.43-3.692.60.0686760.9920.050.0852.65796.2
3.69-4.062.60.0616890.9930.0440.0753.40597.3
4.06-4.652.70.0576740.9920.0410.0713.84297.7
4.65-5.862.80.0587150.9890.0410.0722.85199.3
5.86-502.70.066970.9910.0440.0744.96995.7

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.24data extraction
RefinementResolution: 2.16→32.06 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.906 / SU B: 7.626 / SU ML: 0.189 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.266 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.267 551 4.2 %RANDOM
Rwork0.2026 ---
obs0.2054 12560 94.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 79.26 Å2 / Biso mean: 34.007 Å2 / Biso min: 23.58 Å2
Baniso -1Baniso -2Baniso -3
1--2.16 Å20 Å20.79 Å2
2---1.11 Å20 Å2
3---2.07 Å2
Refinement stepCycle: final / Resolution: 2.16→32.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1757 0 0 46 1803
Biso mean---36.98 -
Num. residues----226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131818
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171574
X-RAY DIFFRACTIONr_angle_refined_deg1.3721.6272477
X-RAY DIFFRACTIONr_angle_other_deg1.3421.5783639
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4835228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.47923.333102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.25515279
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.238159
X-RAY DIFFRACTIONr_chiral_restr0.0620.2234
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022118
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02389
LS refinement shellResolution: 2.16→2.216 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 30 -
Rwork0.289 760 -
all-790 -
obs--79.96 %

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