PDB-6ney: Crystal structure of TcBDF5, a bromodomain containing protein fro...

ID or keywords:

Entry

Database: PDB / ID: 6ney

Title

Crystal structure of TcBDF5, a bromodomain containing protein from Trypanosoma cruzi

Components

Uncharacterized protein

Keywords

TRANSCRIPTION / TcBDF5 / Structural Genomics / Structural Genomics Consortium / SGC

Function / homology

: / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha / Bromo domain-containing protein

Function and homology information

Biological species

Trypanosoma cruzi (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.68 Å

Authors

Loppnau, P. / Dong, A. / Tempel, W. / Lin, Y.H. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Hui, R. / Vedadi, M. / Harding, R.J. / Structural Genomics Consortium (SGC)

Citation

Journal: To Be Published
Title: Crystal structure of TcBDF5, a bromodomain containing protein from Trypanosoma cruzi
Authors: Loppnau, P. / Dong, A. / Tempel, W. / Lin, Y.H. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Hui, R. / Vedadi, M. / Harding, R.J.

History

Deposition	Dec 18, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 20, 2019	Provider: repository / Type: Initial release
Revision 1.1	Oct 11, 2023	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6ney.cif.gz	39 KB	Display	PDBx/mmCIF format
PDB format	pdb6ney.ent.gz	24.4 KB	Display	PDB format
PDBx/mmJSON format	6ney.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6ney_validation.pdf.gz	417.9 KB	Display	wwPDB validaton report
Full document	6ney_full_validation.pdf.gz	418.1 KB	Display
Data in XML	6ney_validation.xml.gz	6.8 KB	Display
Data in CIF	6ney_validation.cif.gz	8.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ne/6ney ftp://data.pdbj.org/pub/pdb/validation_reports/ne/6ney	HTTPS FTP

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Related structure data

Related structure data	5tcmS S: Starting model for refinement
Similar structure data	1gmi-d 5pri-2 5po2-2 5pvj-2 5psq-2 5pog-2 5pv5-2 5pod-2 5ppx-2 5pqu-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Uncharacterized protein

15 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	61.887, 70.428, 26.644
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	Uncharacterized protein Mass: 15047.116 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: C4B63_1g51 / Plasmid: pET15-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-pRARE2 / References: UniProt: A0A2V2W6E9
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 1.93 Å³/Da / Density % sol: 36.25 % / Mosaicity: 0.502 °
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1.8 M NH4SO4, 0.2 M Na Acetate and 0.1M Hepes pH7.5

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97918 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 5, 2018

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97918 Å / Relative weight: 1

Reflection

Resolution: 1.68→50 Å / Num. obs: 13782 / % possible obs: 98.2 % / Redundancy: 7.8 % / R_merge(I) obs: 0.082 / R_pim(I) all: 0.03 / R_rim(I) all: 0.087 / Χ²: 0.951 / Net I/σ(I): 6.6

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.68-1.71	6	0.732	555	0.749	0.283	0.789	0.469	83.7
1.71-1.74	6.2	0.62	636	0.814	0.24	0.669	0.447	90.5
1.74-1.77	6.4	0.55	670	0.886	0.216	0.594	0.448	95.3
1.77-1.81	6.5	0.534	647	0.878	0.213	0.578	0.461	97
1.81-1.85	7	0.409	659	0.958	0.157	0.439	0.474	98.9
1.85-1.89	8	0.381	700	0.95	0.137	0.406	0.493	99.7
1.89-1.94	8.2	0.334	685	0.96	0.119	0.355	0.498	99.9
1.94-1.99	8.3	0.276	695	0.973	0.099	0.293	0.509	99.4
1.99-2.05	8.2	0.229	684	0.979	0.082	0.243	0.691	100
2.05-2.12	8.2	0.185	687	0.984	0.067	0.197	0.672	99.9
2.12-2.19	7.5	0.149	683	0.987	0.057	0.16	0.684	99.7
2.19-2.28	8.5	0.139	698	0.991	0.049	0.148	0.757	99.9
2.28-2.38	8.7	0.109	708	0.995	0.038	0.115	0.85	99.9
2.38-2.51	8.5	0.092	695	0.997	0.033	0.098	0.858	100
2.51-2.67	8.4	0.088	709	0.995	0.031	0.094	1.019	99.6
2.67-2.87	7.8	0.08	695	0.996	0.03	0.086	1.218	99.4
2.87-3.16	8.7	0.073	717	0.997	0.026	0.077	1.466	100
3.16-3.62	8.4	0.065	723	0.997	0.023	0.069	1.915	100
3.62-4.56	7.7	0.058	736	0.998	0.021	0.062	2.086	100
4.56-50	7.5	0.06	800	0.995	0.024	0.065	2.071	99.6

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	3.88 Å	39.52 Å
Translation	3.88 Å	39.52 Å

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0238	refinement
HKL-3000		data scaling
PHASER	2.8.2	phasing
PDB_EXTRACT	3.24	data extraction
HKL-3000		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5TCM

5tcm

Resolution: 1.68→46.49 Å / Cor.coef. F_o:F_c: 0.94 / Cor.coef. F_o:F_c free: 0.925 / SU B: 2.902 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26702	675	4.9 %	RANDOM
R_work	0.22374	-	-	-
obs	0.22603	13004	98.38 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 26.064 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.08 Å²	-0 Å²	0 Å²
2-	-	2.46 Å²	-0 Å²
3-	-	-	-0.38 Å²

Refinement step

Cycle: 1 / Resolution: 1.68→46.49 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	951	0	0	34	985

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.013	968
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	880
X-RAY DIFFRACTION	r_angle_refined_deg	1.502	1.651	1312
X-RAY DIFFRACTION	r_angle_other_deg	1.388	1.574	2031
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.292	5	124
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.278	22.292	48
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.085	15	155
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.422	15	7
X-RAY DIFFRACTION	r_chiral_restr	0.073	0.2	128
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	1101
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	205
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.865	2.772	499
X-RAY DIFFRACTION	r_mcbond_other	1.865	2.768	498
X-RAY DIFFRACTION	r_mcangle_it	2.782	4.144	622
X-RAY DIFFRACTION	r_mcangle_other	2.78	4.149	623
X-RAY DIFFRACTION	r_scbond_it	2.382	3.018	469
X-RAY DIFFRACTION	r_scbond_other	2.38	3.022	470
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	3.532	4.453	690
X-RAY DIFFRACTION	r_long_range_B_refined	4.414	32.888	1080
X-RAY DIFFRACTION	r_long_range_B_other	4.412	32.909	1079
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.68→1.724 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.322	51	-
R_work	0.294	806	-
obs	-	-	87.36 %

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