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- PDB-5ko4: Bromodomain from Trypanosoma brucei Tb427.10.8150 -

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Basic information

Entry
Database: PDB / ID: 5ko4
TitleBromodomain from Trypanosoma brucei Tb427.10.8150
ComponentsPutative uncharacterized protein
KeywordsUNKNOWN FUNCTION / BROMODOMAIN / Structural Genomics Consortium (SGC)
Function / homology
Function and homology information


nuclear lumen / glycosome / nucleus / cytoplasm
Similarity search - Function
Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Bromodomain / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Bromo domain-containing protein
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.44 Å
AuthorsEl Bakkouri, M. / Walker, J.R. / Hou, C.F.D. / Lin, Y.H. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Hui, R. / Structural Genomics Consortium (SGC)
CitationJournal: To be published
Title: Bromodomain from Trypanosoma brucei Tb427.10.8150
Authors: El Bakkouri, M. / Walker, J.R. / Hou, C.F.D. / Lin, Y.H. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Hui, R. / Structural Genomics Consortium (SGC)
History
DepositionJun 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Database references / Structure summary
Revision 1.2Jan 24, 2018Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / pdbx_struct_oper_list
Item: _audit_author.name / _citation_author.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 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: Putative uncharacterized protein
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8495
Polymers25,5612
Non-polymers2883
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-34 kcal/mol
Surface area11480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.374, 52.756, 47.027
Angle α, β, γ (deg.)90.00, 117.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative uncharacterized protein / hypothetical protein


Mass: 12780.618 Da / Num. of mol.: 2 / Fragment: UNP residues 25-130
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (strain 927/4 GUTat10.1) (eukaryote)
Strain: 927/4 GUTat10.1 / Gene: Tb10.6k15.2370 / Plasmid: PET15-MHL / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)-V3R-pRARE2 / References: UniProt: Q38AE9
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.06 Å3/Da / Density % sol: 40.39 % / Mosaicity: 0.42 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: The 12 mg/ml (0.95 mM) protein in the base buffer (100 mM NaCl, 0.5 mM TCEP, 20 mM HEPES pH7,5) was crystallized at 20 ??C in 30% PEGM5K, 0.2 M NH4SO4, 0.1 M MES pH 6.5, in vapor diffusion ...Details: The 12 mg/ml (0.95 mM) protein in the base buffer (100 mM NaCl, 0.5 mM TCEP, 20 mM HEPES pH7,5) was crystallized at 20 ??C in 30% PEGM5K, 0.2 M NH4SO4, 0.1 M MES pH 6.5, in vapor diffusion sitting drop method. Final concentration of 3% DMSO and 1 mM SGC-CBP30 (IUPAC name: 8-(3-chloro-4-methoxy-phenethyl)-4-(3,5-dimethyl-isoxazol-4-yl)-9-(2-(morpholin-4-yl)-propyl)-7,9-diaza-bicyclo[4.3.0]nona-1(6),2,4,7-tetraene) was added to the concentrated protein immediately prior to setting up the crystallization plate.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97901 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97901 Å / Relative weight: 1
ReflectionResolution: 1.44→50 Å / Num. obs: 35635 / % possible obs: 99.2 % / Redundancy: 6.7 % / Biso Wilson estimate: 15.47 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 9.1
Reflection shellResolution: 1.44→1.46 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.358 / % possible all: 96.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
HKL-3000data scaling
PDB_EXTRACT3.2data extraction
HKL-3000data reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3O33

3o33


Resolution: 1.44→41.8 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.956 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.069 / SU Rfree Blow DPI: 0.065 / SU Rfree Cruickshank DPI: 0.062
RfactorNum. reflection% reflectionSelection details
Rfree0.176 1865 5.25 %RANDOM
Rwork0.161 ---
obs0.162 35549 99.2 %-
Displacement parametersBiso mean: 17.65 Å2
Baniso -1Baniso -2Baniso -3
1-0.2775 Å20 Å2-1.3632 Å2
2---1.5866 Å20 Å2
3---1.3092 Å2
Refine analyzeLuzzati coordinate error obs: 0.15 Å
Refinement stepCycle: LAST / Resolution: 1.44→41.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1691 0 15 255 1961
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083764HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.746791HARMONIC3.5
X-RAY DIFFRACTIONt_dihedral_angle_d830SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes42HARMONIC2
X-RAY DIFFRACTIONt_gen_planes577HARMONIC5
X-RAY DIFFRACTIONt_it3764HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.62
X-RAY DIFFRACTIONt_other_torsion14.85
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion247SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4814SEMIHARMONIC4
LS refinement shellResolution: 1.44→1.48 Å / Rfactor Rfree error: 0 / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.188 157 5.52 %
Rwork0.17 2686 -
all0.171 2843 -
obs--97.31 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.35620.29280.02950.45980.33030.4767-0.04380.0304-0.14730.12010.0021-0.08760.2222-0.0240.04170.1427-0.00550.04760.0514-0.0130.09589.66350.279817.8459
20.14270.10260.10720.1470.19330.4349-0.00540.036-0.01780.0131-0.0339-0.00120.1074-0.07540.03920.0908-0.00130.02120.1277-0.02070.041627.82470.47073.5708
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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