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- PDB-5c8g: Crystal Structure Analysis of PP-BRD20 from Tb427tmp complexed wi... -

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Basic information

Entry
Database: PDB / ID: 5c8g
TitleCrystal Structure Analysis of PP-BRD20 from Tb427tmp complexed with BI-2536
ComponentsPP-BRD20
KeywordsGENE REGULATION / Structural Genomics Consortium / SGC / Bromodomain / PP-BRD20 / Tb427tmp
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
Chem-R78 / Bromo domain-containing protein
Similarity search - Component
Biological speciesTrypanosoma brucei gambiense (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsJiang, D.Q. / Tempel, W. / Loppnau, P. / Graslund, S. / Hou, C.F.D. / El Bakkouri, M. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Hui, R. ...Jiang, D.Q. / Tempel, W. / Loppnau, P. / Graslund, S. / Hou, C.F.D. / El Bakkouri, M. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Hui, R. / Amain, M. / Lin, Y.H. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal Structure Analysis of PP-BRD20 from Tb427tmp
Authors: Jiang, D.Q. / Tempel, W. / Loppnau, P. / Graslund, S. / Hou, C.F.D. / El Bakkouri, M. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Hui, R. / Amani, M. / Lin, Y.H.
History
DepositionJun 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PP-BRD20
B: PP-BRD20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,78517
Polymers31,7422
Non-polymers1,04315
Water2,288127
1
A: PP-BRD20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,39213
Polymers15,8711
Non-polymers52212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PP-BRD20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3924
Polymers15,8711
Non-polymers5223
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.092, 53.092, 103.424
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein PP-BRD20 / Chromosome 11 / complete sequence


Mass: 15870.821 Da / Num. of mol.: 2 / Fragment: UNP residues 25-160
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972) (eukaryote)
Strain: MHOM/CI/86/DAL972 / Gene: TbgDal_XI11310 / Plasmid: pET15-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D0A8L1
#2: Chemical ChemComp-R78 / 4-{[(7R)-8-cyclopentyl-7-ethyl-5-methyl-6-oxo-5,6,7,8-tetrahydropteridin-2-yl]amino}-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide


Mass: 521.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H39N7O3
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 13 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.3 Å3/Da / Density % sol: 46.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97957 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97957 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 20890 / % possible obs: 100 % / Redundancy: 5 % / Biso Wilson estimate: 22.3 Å2 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.053 / Rrim(I) all: 0.118 / Χ2: 1.438 / Net I/av σ(I): 19.321 / Net I/σ(I): 6.8 / Num. measured all: 104944
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.95-1.984.90.6610290.8240.330.7390.75299.9
1.98-2.0250.56910400.8560.280.6350.762100
2.02-2.0650.50810310.880.2510.5670.877100
2.06-2.150.44910420.880.2220.5021.764100
2.1-2.1550.36210560.9360.1790.4050.789100
2.15-2.25.10.29810410.9580.1460.3330.83100
2.2-2.2550.33310280.7770.1640.3711.607100
2.25-2.315.10.25110500.9640.1240.280.845100
2.31-2.385.10.20210330.9720.0990.2250.931100
2.38-2.465.10.17210380.9840.0850.1920.887100
2.46-2.545.10.14910440.9860.0730.1670.845100
2.54-2.655.10.12510520.9890.0610.140.84499.9
2.65-2.7750.12310490.9170.0620.1381.096100
2.77-2.9150.110430.9930.0490.1121.026100
2.91-3.15.10.08910440.9920.0440.0991.344100
3.1-3.3350.08610390.9860.0430.0962.045100
3.33-3.6750.08310420.9860.0420.0933.635100
3.67-4.24.90.06810560.9860.0340.0764.156100
4.2-5.294.90.04510640.9980.0220.051.62100
5.29-504.90.04410690.9930.0220.052.18699.4

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Processing

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

4uyg


Resolution: 1.95→30.38 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2396 966 4.63 %
Rwork0.1926 19879 -
obs0.1948 20845 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 61.7 Å2 / Biso mean: 23.2579 Å2 / Biso min: 8 Å2
Refinement stepCycle: final / Resolution: 1.95→30.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1868 0 88 127 2083
Biso mean--16.39 24.46 -
Num. residues----240
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091997
X-RAY DIFFRACTIONf_angle_d0.962720
X-RAY DIFFRACTIONf_chiral_restr0.039289
X-RAY DIFFRACTIONf_plane_restr0.004341
X-RAY DIFFRACTIONf_dihedral_angle_d13.831707
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9504-2.05320.26571380.212428402978
2.0532-2.18180.27851320.21128072939
2.1818-2.35020.28641440.203928392983
2.3502-2.58660.28151320.211128502982
2.5866-2.96060.27371350.208128422977
2.9606-3.7290.24251460.187428242970
3.729-30.38370.18191390.1728773016

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