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- PDB-6nez: Trypanosoma brucei - BDF5, Tb427tmp.01.5000 A, solved with PF-CBP1 -

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Basic information

Entry
Database: PDB / ID: 6nez
TitleTrypanosoma brucei - BDF5, Tb427tmp.01.5000 A, solved with PF-CBP1
ComponentsUncharacterized protein
KeywordsTRANSCRIPTION / Tb427tmp / PF-CBP1 / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology: / Bromodomain / Bromodomain / Bromodomain-like superfamily / nucleoplasm / nucleus / Chem-KJS / Bromo domain-containing protein
Function and homology information
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsLin, Y.H. / Dong, A. / Tempel, W. / McAuley, J. / Loppnau, P. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Hui, R. / Vedadi, M. ...Lin, Y.H. / Dong, A. / Tempel, W. / McAuley, J. / Loppnau, P. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Hui, R. / Vedadi, M. / Harding, R.J. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Trypanosoma brucei - BDF5, Tb427tmp.01.5000 A, solved with PF-CBP1
Authors: Lin, Y.H. / Dong, A. / Tempel, W. / McAuley, J. / Loppnau, P. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Vedadi, M. / Harding, R.J. / Structural Genomics Consortium (SGC)
History
DepositionDec 18, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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
C: Uncharacterized protein
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,21013
Polymers56,2564
Non-polymers1,9549
Water2,036113
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5534
Polymers14,0641
Non-polymers4893
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5534
Polymers14,0641
Non-polymers4893
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5533
Polymers14,0641
Non-polymers4892
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5532
Polymers14,0641
Non-polymers4891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.994, 151.493, 156.180
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Uncharacterized protein


Mass: 14063.993 Da / Num. of mol.: 4
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-CodonPlus(DE3)-RIL / References: UniProt: Q382J7
#2: Chemical
ChemComp-KJS / 5-(3,5-dimethyl-1,2-oxazol-4-yl)-1-[2-(morpholin-4-yl)ethyl]-2-[2-(4-propoxyphenyl)ethyl]-1H-benzimidazole


Mass: 488.621 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C29H36N4O3
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 5 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 3.1 Å3/Da / Density % sol: 60.34 % / Mosaicity: 1.028 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 2.27 M Na Formate, and 0.1M Na Acetate pH4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 35904 / % possible obs: 99.6 % / Redundancy: 8 % / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.037 / Rrim(I) all: 0.106 / Χ2: 0.957 / Net I/σ(I): 6.3 / Num. measured all: 286191
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.247.70.98117430.6880.3591.0480.87999.8
2.24-2.287.90.86817970.6910.3170.9280.86599.7
2.28-2.3280.7517620.7890.2720.8010.85899.9
2.32-2.378.10.66317800.8410.240.7070.87299.8
2.37-2.428.10.56917620.8810.2060.6070.88599.6
2.42-2.4880.50918130.9080.1860.5440.90499.9
2.48-2.547.90.4417600.9260.1620.470.91199.8
2.54-2.617.80.37517560.9530.1410.4020.92899.7
2.61-2.697.10.32917910.9450.130.3550.94398.8
2.69-2.776.70.26817270.9610.1090.2911.00898.2
2.77-2.878.40.22517910.9830.0810.240.99299.8
2.87-2.9990.17118080.990.0580.1810.99299.9
2.99-3.129.20.14617960.9930.050.1541.02599.8
3.12-3.299.10.11517880.9950.0390.1221.03699.8
3.29-3.498.90.08418070.9970.0290.0891.02899.9
3.49-3.768.40.06618170.9980.0240.0711.011100
3.76-4.147.80.05218120.9980.0190.0560.96599.9
4.14-4.746.90.04718380.9980.0190.0510.99299.9
4.74-5.976.80.04818190.9980.0190.0521.0198.3
5.97-507.60.04319370.9970.0170.047199

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.54 Å42.9 Å
Translation2.54 Å42.9 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-3000data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K29

5k29


Resolution: 2.2→42.94 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / SU B: 6.422 / SU ML: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.201 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2458 1087 3 %RANDOM
Rwork0.2045 ---
obs0.2058 34783 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 107.12 Å2 / Biso mean: 42.996 Å2 / Biso min: 28.69 Å2
Baniso -1Baniso -2Baniso -3
1-1.88 Å20 Å2-0 Å2
2--0.47 Å20 Å2
3----2.35 Å2
Refinement stepCycle: final / Resolution: 2.2→42.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3559 0 130 113 3802
Biso mean--53.08 40.86 -
Num. residues----463
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133763
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173437
X-RAY DIFFRACTIONr_angle_refined_deg1.4921.6385101
X-RAY DIFFRACTIONr_angle_other_deg1.3141.6247935
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4165461
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.65822.323198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.94715596
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8821527
X-RAY DIFFRACTIONr_chiral_restr0.0690.2478
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024603
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02790
LS refinement shellResolution: 2.198→2.255 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 83 -
Rwork0.299 2474 -
all-2557 -
obs--97.3 %

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