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- PDB-7dl8: Crystal structure of ALBA1 from Trypanosoma brucei -

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Basic information

Entry
Database: PDB / ID: 7dl8
TitleCrystal structure of ALBA1 from Trypanosoma brucei
ComponentsALBA-Domain Protein
KeywordsRNA BINDING PROTEIN / ALBA domain / RNA binding
Function / homology
Function and homology information


nucleic acid binding
Similarity search - Function
Uncharacterised conserved protein UCP030333, DNA/RNA-binding Alba-related / Alba-like domain / DNA/RNA-binding protein Alba-like / Alba / Alba-like domain superfamily / Translation Initiation Factor IF3 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.459 Å
AuthorsLiao, S. / Gao, J. / Tu, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31500601 China
CitationJournal: J.Struct.Biol. / Year: 2021
Title: Crystal structure of TbAlba1 from Trypanosoma brucei.
Authors: Gao, J. / Xiao, C. / Liao, S. / Tu, X.
History
DepositionNov 26, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALBA-Domain Protein
B: ALBA-Domain Protein
C: ALBA-Domain Protein
D: ALBA-Domain Protein


Theoretical massNumber of molelcules
Total (without water)61,0614
Polymers61,0614
Non-polymers00
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-23 kcal/mol
Surface area22810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.028, 86.236, 211.259
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-211-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 11 and (name N or name...
21(chain B and ((resid 11 and (name N or name...
31(chain C and (resid 11 through 23 or resid 25...
41(chain D and (resid 11 through 18 or (resid 19...

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
11ARGARGARGARG(chain A and ((resid 11 and (name N or name...AA1111
12ASPASPALAALA(chain A and ((resid 11 and (name N or name...AA8 - 1268 - 126
13ASPASPALAALA(chain A and ((resid 11 and (name N or name...AA8 - 1268 - 126
14ASPASPALAALA(chain A and ((resid 11 and (name N or name...AA8 - 1268 - 126
15ASPASPALAALA(chain A and ((resid 11 and (name N or name...AA8 - 1268 - 126
21ARGARGARGARG(chain B and ((resid 11 and (name N or name...BB1111
22ARGARGTHRTHR(chain B and ((resid 11 and (name N or name...BB9 - 1259 - 125
23ARGARGTHRTHR(chain B and ((resid 11 and (name N or name...BB9 - 1259 - 125
24ARGARGTHRTHR(chain B and ((resid 11 and (name N or name...BB9 - 1259 - 125
25ARGARGTHRTHR(chain B and ((resid 11 and (name N or name...BB9 - 1259 - 125
31ARGARGPHEPHE(chain C and (resid 11 through 23 or resid 25...CC11 - 2311 - 23
32PHEPHEGLNGLN(chain C and (resid 11 through 23 or resid 25...CC25 - 6225 - 62
33GLNGLNGLNGLN(chain C and (resid 11 through 23 or resid 25...CC6363
34PROPROARGARG(chain C and (resid 11 through 23 or resid 25...CC10 - 11310 - 113
35PROPROARGARG(chain C and (resid 11 through 23 or resid 25...CC10 - 11310 - 113
36PROPROARGARG(chain C and (resid 11 through 23 or resid 25...CC10 - 11310 - 113
37PROPROARGARG(chain C and (resid 11 through 23 or resid 25...CC10 - 11310 - 113
38PROPROPROPRO(chain C and (resid 11 through 23 or resid 25...CC8484
39PROPROARGARG(chain C and (resid 11 through 23 or resid 25...CC10 - 11310 - 113
310PROPROARGARG(chain C and (resid 11 through 23 or resid 25...CC10 - 11310 - 113
311PROPROARGARG(chain C and (resid 11 through 23 or resid 25...CC10 - 11310 - 113
312PROPROARGARG(chain C and (resid 11 through 23 or resid 25...CC10 - 11310 - 113
41ARGARGTYRTYR(chain D and (resid 11 through 18 or (resid 19...DD11 - 1811 - 18
42ARGARGARGARG(chain D and (resid 11 through 18 or (resid 19...DD1919
43ARGARGTHRTHR(chain D and (resid 11 through 18 or (resid 19...DD11 - 12511 - 125
44ARGARGTHRTHR(chain D and (resid 11 through 18 or (resid 19...DD11 - 12511 - 125
45ARGARGTHRTHR(chain D and (resid 11 through 18 or (resid 19...DD11 - 12511 - 125
46ARGARGTHRTHR(chain D and (resid 11 through 18 or (resid 19...DD11 - 12511 - 125

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Components

#1: Protein
ALBA-Domain Protein


Mass: 15265.312 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: ALBA1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A3L6KSX9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.61 Å3/Da / Density % sol: 52.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2M Potassium sodium tartrate tetrahydrate, 0.1M Sodium citrate tribasic dihydrate pH 5.6, 2.0M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.459→50 Å / Num. obs: 23706 / % possible obs: 99.8 % / Redundancy: 13.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Net I/σ(I): 18.9
Reflection shellResolution: 2.46→2.55 Å / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 2342 / CC1/2: 0.953

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: rosetta model

Resolution: 2.459→43.118 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2613 1890 8.42 %
Rwork0.2379 41115 -
obs0.2399 23686 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123.54 Å2 / Biso mean: 60.0264 Å2 / Biso min: 33.29 Å2
Refinement stepCycle: final / Resolution: 2.459→43.118 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3193 0 0 28 3221
Biso mean---57.24 -
Num. residues----431
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1112X-RAY DIFFRACTION9.758TORSIONAL
12B1112X-RAY DIFFRACTION9.758TORSIONAL
13C1112X-RAY DIFFRACTION9.758TORSIONAL
14D1112X-RAY DIFFRACTION9.758TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.46-2.490.38951410.33631526100
2.49-2.52280.29571440.31731553100
2.5228-2.55730.34211350.29451452100
2.5573-2.59380.38141410.30681540100
2.5938-2.63250.3451420.29551552100
2.6325-2.67370.3631310.30021499100
2.6737-2.71750.31081430.29081521100
2.7175-2.76440.28211450.29091565100
2.7644-2.81460.26121340.28851504100
2.8146-2.86870.35091370.29991497100
2.8687-2.92730.34781470.27491575100
2.9273-2.99090.34731390.28271490100
2.9909-3.06050.29121410.26971546100
3.0605-3.1370.32131340.27381490100
3.137-3.22180.28421430.25551519100
3.2218-3.31660.27331420.24941549100
3.3166-3.42360.31551420.24661520100
3.4236-3.54590.26411350.24651510100
3.5459-3.68780.24121450.23091540100
3.6878-3.85550.27631330.20981503100
3.8555-4.05860.2641390.22971536100
4.0586-4.31270.20661480.19841536100
4.3127-4.64530.19711410.19261523100
4.6453-5.11210.21081470.18891495100
5.1121-5.85030.29011370.25371527100
5.8503-7.36480.26791360.25191510100
7.3648-43.1180.18581370.2018153799
Refinement TLS params.Method: refined / Origin x: 1.0051 Å / Origin y: 17.2199 Å / Origin z: -23.4792 Å
111213212223313233
T0.4414 Å20.055 Å20.0032 Å2-0.3759 Å20.0235 Å2--0.3758 Å2
L0.3242 °2-0.191 °20.3481 °2-0.5577 °2-0.2853 °2--0.714 °2
S0.0389 Å °0.051 Å °-0.0147 Å °-0.0231 Å °-0.0463 Å °0.0275 Å °-0.0669 Å °0.0522 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA8 - 126
2X-RAY DIFFRACTION1allB9 - 125
3X-RAY DIFFRACTION1allC10 - 113
4X-RAY DIFFRACTION1allD11 - 125
5X-RAY DIFFRACTION1allS1 - 33

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