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- PDB-5fea: Domain Swapped Bromodomain from Leishmania donovani -

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Basic information

Entry
Database: PDB / ID: 5fea
TitleDomain Swapped Bromodomain from Leishmania donovani
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / BROMODOMAIN / DOMAIN-SWAPPING / BROMOSPORINE / Structural Genomics Consortium (SGC)
Function / homology
Function and homology information


Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Bromosporine / BROMIDE ION / Bromodomain family protein
Similarity search - Component
Biological speciesLeishmania donovani (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsWalker, J.R. / Hou, C.F.D. / Lin, Y.H. / LOPPNAU, P. / Dong, A. / El Bakkouri, M. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Hui, R. / Structural Genomics Consortium (SGC)
CitationJournal: To be published
Title: Domain Swapped Bromodomain from Leishmania donovani
Authors: Walker, J.R. / Hou, C.F.D. / Lin, Y.H. / LOPPNAU, P. / Dong, A. / El Bakkouri, M. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Hui, R. / Structural Genomics Consortium (SGC)
History
DepositionDec 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 27, 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: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3726
Polymers31,4032
Non-polymers9694
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6720 Å2
ΔGint-69 kcal/mol
Surface area13830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.176, 77.176, 169.496
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A9 - 124
2010B9 - 124

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Components

#1: Protein Uncharacterized protein


Mass: 15701.688 Da / Num. of mol.: 2 / Fragment: Bromodomain, UNP residues 25-160
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania donovani (strain BPK282A1) (eukaryote)
Strain: BPK282A1 / Gene: LDBPK_363520 / Plasmid: PET15-MHL / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: E9BU61
#2: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.32 Å3/Da / Density % sol: 46.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: The protein (concentrated to 15mg/mL in 20mM HEPES pH 7.5 and 150 mM NaCl) was crystallized at 293 K in 30% PEG2000 MME, 0.15M KBr with bromosporine using the sitting drop method.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 9764 / % possible obs: 98.9 % / Redundancy: 17.7 % / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.025 / Rrim(I) all: 0.102 / Χ2: 1.578 / Net I/av σ(I): 40.25 / Net I/σ(I): 10.1 / Num. measured all: 173005
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.6418.70.6984540.9840.1650.7181.48298.5
2.64-2.6918.40.6684790.9620.1590.6871.58898.6
2.69-2.7418.50.6074610.9790.1440.6251.52598.9
2.74-2.818.30.5044790.9820.120.5191.47999.2
2.8-2.8618.60.4334730.9890.1030.4451.54299.2
2.86-2.9318.40.3534670.9920.0840.3631.53598.3
2.93-318.30.2984780.9950.0710.3061.55599.2
3-3.0818.50.2674750.9930.0640.2741.62499
3.08-3.1718.10.1894710.9970.0460.1951.62199.2
3.17-3.2818.20.1694900.9980.0410.1741.58499
3.28-3.3918.10.1284730.9980.0310.1321.68699.2
3.39-3.5317.70.1134970.9980.0270.1161.80899.4
3.53-3.6917.90.1154750.9980.0280.1191.92599
3.69-3.8817.40.0984970.9980.0250.1011.99499.4
3.88-4.1317.40.0864760.9970.0210.0891.98699.6
4.13-4.4517.30.0715030.9990.0180.0741.91399.4
4.45-4.8916.70.0625040.9990.0160.0651.46399.2
4.89-5.6170.0585150.9980.0140.061.14799.2
5.6-7.0516.90.0545190.9990.0140.0561.07198.9
7.05-50150.0525780.9980.0140.0541.0596.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-2000data scaling
PHASERphasing
REFMAC5.8.0124refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C8G

5c8g


Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.897 / SU B: 25.12 / SU ML: 0.281 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.802 / ESU R Free: 0.344 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2772 515 5.3 %RANDOM
Rwork0.2275 ---
obs0.23 9220 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 134.62 Å2 / Biso mean: 69.331 Å2 / Biso min: 38.18 Å2
Baniso -1Baniso -2Baniso -3
1-2.15 Å21.08 Å20 Å2
2--2.15 Å20 Å2
3----6.99 Å2
Refinement stepCycle: final / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1935 0 58 18 2011
Biso mean--55.32 53.2 -
Num. residues----246
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192049
X-RAY DIFFRACTIONr_bond_other_d0.0040.021868
X-RAY DIFFRACTIONr_angle_refined_deg1.1361.9242799
X-RAY DIFFRACTIONr_angle_other_deg1.0634260
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0695246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.77623.22693
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.9215317
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.6541515
X-RAY DIFFRACTIONr_chiral_restr0.0640.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022524
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02493
X-RAY DIFFRACTIONr_mcbond_it1.0294.207987
X-RAY DIFFRACTIONr_mcbond_other1.0284.207986
X-RAY DIFFRACTIONr_mcangle_it1.736.3091232
Refine LS restraints NCS

Ens-ID: 1 / Number: 11116 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 41 -
Rwork0.276 656 -
all-697 -
obs--99.01 %
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)
13.79540.8979-0.61133.6536-1.80133.85990.23280.1960.7186-0.0154-0.14020.1555-0.1056-0.1327-0.09270.1660.1772-0.03010.3145-0.01910.2002-18.7816-24.320112.2835
23.8746-1.2518-0.76974.0172-4.391916.79290.04360.1719-0.1906-0.3237-0.13310.04070.2590.22870.08950.13410.1125-0.00520.25030.01920.2619-6.9791-33.700514.4354
34.3172-3.5483-1.13057.02791.55090.41840.21520.1457-0.4017-0.1695-0.35150.1169-0.0192-0.01220.13630.10850.19410.04420.37840.10570.1778-0.217-57.624615.8181
45.727-2.0527-1.88414.56671.5483.89820.08040.7283-0.161-0.3913-0.1352-0.5297-0.12580.20040.05480.29040.31550.14450.5520.09350.13374.8117-50.42315.0111
515.1091-4.48492.46551.3413-0.73510.4042-0.2236-0.7786-0.51090.07020.27810.1042-0.0387-0.1263-0.05450.5480.0258-0.0630.55040.05580.459215.628-63.12517.8165
64.0281-2.6853-0.95087.20412.84351.13410.1445-0.1488-0.1938-0.29450.0498-0.5407-0.12160.0346-0.19430.18040.20320.03680.37060.15480.21997.6627-48.236317.0779
74.2478-1.84760.69783.85830.49022.8672-0.079-0.21740.50880.2302-0.0734-0.368-0.33670.31170.15240.14030.0590.00350.29960.08820.1882-4.3599-21.857317.5756
86.86840.21848.08678.8474-5.714313.84650.070.69010.7481-0.4137-0.58880.61890.1710.75230.51880.19620.38170.02520.94630.03880.1995-4.6732-22.61121.8178
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 58
2X-RAY DIFFRACTION2A59 - 75
3X-RAY DIFFRACTION3A76 - 115
4X-RAY DIFFRACTION4A116 - 149
5X-RAY DIFFRACTION5B33 - 45
6X-RAY DIFFRACTION6B46 - 80
7X-RAY DIFFRACTION7B81 - 128
8X-RAY DIFFRACTION8B129 - 153

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