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- PDB-5k29: Trypanosoma brucei bromodomain BDF5 (Tb427tmp.01.5000) -

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Basic information

Entry
Database: PDB / ID: 5k29
TitleTrypanosoma brucei bromodomain BDF5 (Tb427tmp.01.5000)
Componentsuncharacterized protein BDF5
KeywordsStructural Genomics / Unknown Function / bromodomain / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


nucleoplasm / nucleus
Similarity search - Function
: / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain / Bromodomain / Bromodomain-like superfamily / 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 / SAD / Resolution: 2.1 Å
AuthorsLin, Y.H. / Tempel, W. / Walker, J.R. / Loppnau, P. / Amani, M. / Hou, C.F.D. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. ...Lin, Y.H. / Tempel, W. / Walker, J.R. / Loppnau, P. / Amani, M. / Hou, C.F.D. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Hui, R. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: Trypanosoma brucei bromodomain BDF5 (Tb427tmp.01.5000)
Authors: Lin, Y.H. / Tempel, W. / Walker, J.R. / Loppnau, P. / Amani, M. / Hou, C.F.D. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Hui, R.
History
DepositionMay 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Structure summary
Revision 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: uncharacterized protein BDF5
B: uncharacterized protein BDF5


Theoretical massNumber of molelcules
Total (without water)28,2429
Polymers28,2422
Non-polymers07
Water27015
1
A: uncharacterized protein BDF5


Theoretical massNumber of molelcules
Total (without water)14,1212
Polymers14,1211
Non-polymers01
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: uncharacterized protein BDF5


Theoretical massNumber of molelcules
Total (without water)14,1217
Polymers14,1211
Non-polymers06
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.358, 41.020, 53.067
Angle α, β, γ (deg.)90.000, 111.390, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein uncharacterized protein BDF5


Mass: 14121.044 Da / Num. of mol.: 2 / Fragment: bromo domain
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: Tb11.01.5000 / Plasmid: pET15-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-T1R-pACYC LamP / References: UniProt: Q382J7
#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 7 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.91 Å3/Da / Density % sol: 35.76 % / Mosaicity: 0.21 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 12% PEG-3350, 0.1M DL-Malic acid. 0.001 M Bromosporine was also added but not located in the electron density.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→49.68 Å / Num. obs: 12642 / % possible obs: 99.5 % / Redundancy: 3.7 % / Biso Wilson estimate: 50.19 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.029 / Rrim(I) all: 0.055 / Net I/σ(I): 14.3 / Num. measured all: 46818
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 3.8 % / Rmerge(I) obs: 1.092 / Mean I/σ(I) obs: 1.4 / Num. measured all: 3992 / Num. unique all: 1061 / CC1/2: 0.745 / Rpim(I) all: 0.654 / Rrim(I) all: 1.276 / Rejects: 0 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER-TNT2.10.2refinement
Aimless0.5.24data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
XDSdata scaling
BUCCANEERmodel building
PHASERphasing
SHELXDEphasing
ARPmodel building
WARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.1→49.41 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.947 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.173 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.169 / SU Rfree Blow DPI: 0.15 / SU Rfree Cruickshank DPI: 0.153
Details: The structure was solved by SAD with a nearly isomorphous selenomethionyl derivative and the CCP4 SHELX-PHASER-PARROT-BUCCANEER pipeline. ARP/WARP in atom update and autobuild modes with the ...Details: The structure was solved by SAD with a nearly isomorphous selenomethionyl derivative and the CCP4 SHELX-PHASER-PARROT-BUCCANEER pipeline. ARP/WARP in atom update and autobuild modes with the current native data gave a model that was further refined with REFMAC and BUSTER.
RfactorNum. reflection% reflection
Rfree0.223 1225 9.7 %
Rwork0.191 --
obs0.194 12631 99.4 %
Displacement parametersBiso max: 155.2 Å2 / Biso mean: 72.06 Å2 / Biso min: 35.92 Å2
Baniso -1Baniso -2Baniso -3
1--3.7765 Å20 Å215.7011 Å2
2--5.05 Å20 Å2
3----1.2735 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: final / Resolution: 2.1→49.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1311 0 7 15 1333
Biso mean--67.64 62.92 -
Num. residues----183
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d464SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes28HARMONIC2
X-RAY DIFFRACTIONt_gen_planes206HARMONIC5
X-RAY DIFFRACTIONt_it1346HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion186SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance3HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1542SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1346HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg1819HARMONIC20.96
X-RAY DIFFRACTIONt_omega_torsion2.48
X-RAY DIFFRACTIONt_other_torsion16.64
LS refinement shellResolution: 2.1→2.3 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.213 319 10.58 %
Rwork0.192 2696 -
all-3015 -
obs--99.87 %
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)
13.7156-1.28771.787.25281.83375.7480.0207-0.06280.38240.0496-0.23940.0957-0.1199-0.53290.2187-0.13770.0278-0.1219-0.10720.0093-0.1083-5.82845.560534.3399
25.0478-0.71171.95636.2534-2.29258.418-0.0797-0.2415-0.2098-0.348-0.20190.45830.4612-0.42790.2816-0.0815-0.0103-0.0661-0.171-0.108-0.0786-27.58557.043913.2856
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A5 - 123
2X-RAY DIFFRACTION2{ B|* }B5 - 121

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