[English] 日本語
Yorodumi
- PDB-7dl8: Crystal structure of ALBA1 from Trypanosoma brucei -

+
Open data


ID or keywords:

Loading...

-
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 / homologyUncharacterised conserved protein UCP030333, DNA/RNA-binding Alba-related / DNA/RNA-binding protein Alba-like / Alba / Alba-like domain superfamily / nucleic acid binding / ALBA-Domain Protein
Function and homology information
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more