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- PDB-5c4q: Crystal Structure Analysis of bromodomain from Leishmania donovan... -

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Basic information

Entry
Database: PDB / ID: 5c4q
TitleCrystal Structure Analysis of bromodomain from Leishmania donovani complexed with bromosporine
ComponentsBromodomain
KeywordsTRANSCRIPTION / Structural Genomics Consortium / SGC / Bromodomain / Bromosporine / Leishmania donovani
Function / homology
Function and homology information


Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Bromosporine / Bromo domain-containing protein
Similarity search - Component
Biological speciesLeishmania donovani (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.932 Å
AuthorsJiang, D.Q. / Tempel, W. / Loppnau, P. / Graslund, S. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Hui, R. / Amani, M. / Hou, C.F.D. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal Structure Analysis of bromodomain from Leishmania donovani complexed with bromosporine
Authors: Jiang, D.Q. / Tempel, W. / Loppnau, P. / Graslund, S. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Hui, R. / Amani, M. / Hou, C.F.D.
History
DepositionJun 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / 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
B: Bromodomain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,69013
Polymers28,8812
Non-polymers80911
Water2,522140
1
A: Bromodomain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8456
Polymers14,4401
Non-polymers4045
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8457
Polymers14,4401
Non-polymers4046
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-6 kcal/mol
Surface area12530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.916, 34.385, 86.463
Angle α, β, γ (deg.)90.000, 117.580, 90.000
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly of the protein indicated by Mass spectrometry and Gel filtration is monomer.

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Components

#1: Protein Bromodomain /


Mass: 14440.311 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania donovani (strain BPK282A1) (eukaryote)
Strain: BPK282A1 / Gene: LDBPK_363130 / Plasmid: V3R pRARE2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E9BU22
#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-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 9 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.03 Å3/Da / Density % sol: 39.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.4 M sodium malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.93→20 Å / Num. obs: 16741 / % possible obs: 94.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 23.97 Å2 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.055 / Rrim(I) all: 0.109 / Χ2: 1.524 / Net I/av σ(I): 14.418 / Net I/σ(I): 7.2 / Num. measured all: 61331
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.93-1.9620.4455380.7560.3290.5570.67661.6
1.96-22.30.3866440.7890.2780.4790.70672.6
2-2.042.70.3797020.8520.2530.4590.67282
2.04-2.082.90.3377730.8840.2160.4030.6990
2.08-2.123.20.3228470.8840.20.3810.73495.1
2.12-2.173.50.3298460.9260.1970.3851.47397.1
2.17-2.233.70.2498530.9430.1480.290.75599.6
2.23-2.293.80.238950.950.1340.2670.85599.6
2.29-2.3640.2328550.9530.1340.2680.88999.8
2.36-2.4340.1978930.9580.1140.2290.944100
2.43-2.5240.1688610.970.0960.1940.84799.8
2.52-2.6240.1619030.9730.0930.1860.966100
2.62-2.7440.1428570.9820.0810.1640.976100
2.74-2.8840.1168750.9850.0660.1351.147100
2.88-3.0640.0988850.9890.0560.1141.298100
3.06-3.340.088870.9880.0450.0921.973100
3.3-3.6340.0668870.9880.0380.0772.595100
3.63-4.1540.0628980.990.0360.0723.432100
4.15-5.2140.0529080.9960.0290.062.898100
5.21-203.80.0559340.9960.0320.0633.43299.5

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HBW

4hbw


Resolution: 1.932→19.16 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.06 / Stereochemistry target values: ML
Details: Bromosporine restraints generated by PHENIX.ELBOW were modified to restrain coordinates of the lactamate moiety in a single plane, prompted by a MOGUL query of related structures in the ...Details: Bromosporine restraints generated by PHENIX.ELBOW were modified to restrain coordinates of the lactamate moiety in a single plane, prompted by a MOGUL query of related structures in the Cambridge Structural Database.
RfactorNum. reflection% reflection
Rfree0.2398 802 4.79 %
Rwork0.1814 15936 -
obs0.1842 16738 94.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.05 Å2 / Biso mean: 23.9427 Å2 / Biso min: 10.67 Å2
Refinement stepCycle: final / Resolution: 1.932→19.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1826 0 91 140 2057
Biso mean--26.04 28 -
Num. residues----232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121971
X-RAY DIFFRACTIONf_angle_d1.0322691
X-RAY DIFFRACTIONf_chiral_restr0.037287
X-RAY DIFFRACTIONf_plane_restr0.005339
X-RAY DIFFRACTIONf_dihedral_angle_d14.493698
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9324-2.05340.3057990.23641990208972
2.0534-2.21170.27511210.20032674279596
2.2117-2.43390.25611360.191827902926100
2.4339-2.78510.28561760.201527602936100
2.7851-3.50550.26991300.180128182948100
3.5055-19.16060.17461400.158129043044100

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