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- PDB-5tck: Second Bromodomain from Leishmania donovani LdBPK.091320 complexe... -

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Basic information

Entry
Database: PDB / ID: 5tck
TitleSecond Bromodomain from Leishmania donovani LdBPK.091320 complexed with Bromosporine
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / Bromodomain / Structural Genomics Consortium (SGC)
Function / homology: / Bromodomain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / BETA-MERCAPTOETHANOL / Bromosporine / SULFUR OXIDE / Bromodomain family protein
Function and homology information
Biological speciesLeishmania donovani (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLin, L.-H. / Hou, C.F.D. / Loppnau, P. / Dong, A. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Hui, R. / Walker, J.R. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: Second Bromodomain from Leishmania donovani LdBPK.091320 complexed with Bromosporine
Authors: Lin, L.-H. / Hou, C.F.D. / Loppnau, P. / Dong, A. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Hui, R. / Walker, J.R. / Structural Genomics Consortium (SGC)
History
DepositionSep 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 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 1.2Apr 2, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details
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: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,10410
Polymers35,9192
Non-polymers1,1858
Water3,081171
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5525
Polymers17,9591
Non-polymers5934
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5525
Polymers17,9591
Non-polymers5934
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.245, 74.086, 106.412
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Uncharacterized protein


Mass: 17959.279 Da / Num. of mol.: 2 / Fragment: UNP residues 161-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania donovani (strain BPK282A1) (eukaryote)
Strain: BPK282A1 / Gene: LDBPK_091320 / Plasmid: pET15-MHL / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21-CodonPlus-RIL / References: UniProt: E9BA17

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Non-polymers , 5 types, 179 molecules

#2: 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.: 2 / Source method: obtained synthetically / Formula: C17H20N6O4S
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-SX / SULFUR OXIDE


Mass: 48.064 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: OS
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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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: 1.88 Å3/Da / Density % sol: 34.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: The protein was crystallized at 293 K with 1% w/v Tryptone, 0.001 M Sodium azide, 0.05 M HEPES sodium pH 7.0, 12% w/v Polyethylene glycol 3,350 with Bromosporine using the sitting drop method.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Jun 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 20521 / % possible obs: 99.7 % / Redundancy: 7.2 % / Biso Wilson estimate: 36.86 Å2 / Net I/σ(I): 24.5

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
HKL-3000data reduction
HKL-3000data scaling
Arcimboldophasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→26.84 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.935 / SU R Cruickshank DPI: 0.441 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.2 / SU Rfree Blow DPI: 0.166 / SU Rfree Cruickshank DPI: 0.161
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1020 5 %RANDOM
Rwork0.196 ---
obs0.198 20392 99.6 %-
Displacement parametersBiso mean: 39.75 Å2
Baniso -1Baniso -2Baniso -3
1--3.3466 Å20 Å20 Å2
2---0.3451 Å20 Å2
3---3.6918 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: 1 / Resolution: 1.95→26.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2161 0 76 171 2408
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0094512HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.628064HARMONIC3.8
X-RAY DIFFRACTIONt_dihedral_angle_d997SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes50HARMONIC2
X-RAY DIFFRACTIONt_gen_planes735HARMONIC5
X-RAY DIFFRACTIONt_it4512HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.27
X-RAY DIFFRACTIONt_other_torsion14.15
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion296SEMIHARMONIC5
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_contact5144SEMIHARMONIC4
LS refinement shellResolution: 1.95→2.06 Å / Rfactor Rfree error: 0 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.249 137 4.75 %
Rwork0.211 2750 -
all0.213 2887 -
obs--98.76 %
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)
10.70860.1985-0.04262.23510.27521.01820.0112-0.04430.01520.03020.01110.01040.0894-0.0495-0.0223-0.2874-0.03380.0177-0.30520.0038-0.346915.791855.803515.5496
20.28610.55620.15931.25370.42630.08-0.03110.01720.0429-0.11580.01520.1210.01320.00490.01590.09360.0177-0.01350.12160.01110.08732.963783.61265.3673
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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