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- PDB-6if4: Crystal structure of Tbtudor -

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Basic information

Entry
Database: PDB / ID: 6if4
TitleCrystal structure of Tbtudor
ComponentsHistone acetyltransferase
KeywordsDNA BINDING PROTEIN / Tudor / DNA / transcription / methylation
Function / homology
Function and homology information


histone acetyltransferase activity / transcription coregulator activity / histone binding / negative regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Histone acetyltransferase domain, MYST-type / MOZ/SAS family / MYST-type histone acetyltransferase (HAT) domain profile. / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / Chromo-like domain superfamily / Acyl-CoA N-acyltransferase / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Histone acetyltransferase, putative
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.934 Å
AuthorsGao, J. / Ye, K. / Diwu, Y. / Liao, S. / Tu, X.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China31500601 China
National Natural Science Foundation of ChinaU1332137 China
National Natural Science Foundation of China31570737 China
CitationJournal: J.Struct.Biol. / Year: 2020
Title: Crystal structure of TbEsa1 presumed Tudor domain from Trypanosoma brucei.
Authors: Gao, J. / Ye, K. / Diwu, Y. / Xu, C. / Zhang, X. / Liao, S. / Tu, X.
History
DepositionSep 18, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 2.0Nov 6, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_sites / computing / diffrn / entity / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / software / struct_ncs_dom / struct_ncs_dom_lim / struct_sheet_range
Item: _atom_sites.fract_transf_matrix[1][2] / _atom_sites.fract_transf_matrix[1][3] ..._atom_sites.fract_transf_matrix[1][2] / _atom_sites.fract_transf_matrix[1][3] / _atom_sites.fract_transf_matrix[2][3] / _atom_sites.fract_transf_matrix[3][3] / _diffrn.pdbx_serial_crystal_experiment / _entity.pdbx_number_of_molecules / _pdbx_struct_assembly_gen.asym_id_list / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_work / _refine.overall_SU_ML / _refine.pdbx_ls_cross_valid_method / _refine.pdbx_overall_phase_error / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.cycle_id / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_protein / _refine_hist.pdbx_number_residues_total / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_free_error / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _software.version / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id
Description: Atomic clashes / Provider: author / Type: Coordinate replacement
Revision 2.1Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.2Nov 22, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Histone acetyltransferase
A: Histone acetyltransferase


Theoretical massNumber of molelcules
Total (without water)17,1392
Polymers17,1392
Non-polymers00
Water1,33374
1
A: Histone acetyltransferase


Theoretical massNumber of molelcules
Total (without water)8,5701
Polymers8,5701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone acetyltransferase


Theoretical massNumber of molelcules
Total (without water)8,5701
Polymers8,5701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.389, 34.274, 37.470
Angle α, β, γ (deg.)113.580, 100.530, 102.900
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 14 or (resid 15...
21(chain B and (resid 2 through 30 or (resid 31...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALLEULEU(chain A and (resid 2 through 14 or (resid 15...AB2 - 142 - 14
12HISHISHISHIS(chain A and (resid 2 through 14 or (resid 15...AB1515
13VALVALARGARG(chain A and (resid 2 through 14 or (resid 15...AB2 - 612 - 61
21VALVALALAALA(chain B and (resid 2 through 30 or (resid 31...BA2 - 302 - 30
22HISHISHISHIS(chain B and (resid 2 through 30 or (resid 31...BA3131
23METMETARGARG(chain B and (resid 2 through 30 or (resid 31...BA1 - 611 - 61
24METMETARGARG(chain B and (resid 2 through 30 or (resid 31...BA1 - 611 - 61
25METMETARGARG(chain B and (resid 2 through 30 or (resid 31...BA1 - 611 - 61

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Components

#1: Protein Histone acetyltransferase / / Tbtudor


Mass: 8569.652 Da / Num. of mol.: 2
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: Tb927.7.4560 / Production host: Enterobacteria phage L1 (virus) / References: UniProt: D6XIY7, histone acetyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 1.87 Å3/Da / Density % sol: 34.36 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1M Bis-Tris, 3M NaCl pH6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.93→32.71 Å / Num. obs: 8625 / % possible obs: 92.6 % / Redundancy: 3.8 % / CC1/2: 0.995 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.068 / Rrim(I) all: 0.134 / Net I/σ(I): 8.9
Reflection shellResolution: 1.93→2.04 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.652 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1246 / CC1/2: 0.78 / Rpim(I) all: 0.391 / Rrim(I) all: 0.761 / % possible all: 91.8

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PL6

4pl6


Resolution: 1.934→32.71 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 27.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2488 429 4.98 %
Rwork0.2064 8193 -
obs0.2084 8622 92.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.84 Å2 / Biso mean: 28.9127 Å2 / Biso min: 11.55 Å2
Refinement stepCycle: final / Resolution: 1.934→32.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms986 0 0 74 1060
Biso mean---33.21 -
Num. residues----121
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A538X-RAY DIFFRACTION15.771TORSIONAL
12B538X-RAY DIFFRACTION15.771TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.934-2.21360.30251470.2416268191
2.2136-2.78870.28941470.2367275594
2.7887-32.710.21081350.1837275793

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