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- PDB-6fsw: Structure of Archaeoglobus fulgidus SBDS protein at 1.9 Angstrom -

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Basic information

Entry
Database: PDB / ID: 6fsw
TitleStructure of Archaeoglobus fulgidus SBDS protein at 1.9 Angstrom
ComponentsRibosome maturation protein SDO1-like protein
KeywordsRIBOSOMAL PROTEIN / SBDS / conformational flexibility
Function / homology
Function and homology information


cytosolic ribosome assembly
Similarity search - Function
SBDS protein C-terminal domain, subdomain 1 / Hypothetical 12.0 Kda Protein In Nam8-gar1 Intergenic Region; Chain: A; / Ribosome maturation protein SBDS, N-terminal domain / Ribosome maturation protein SDO1/SBDS, C-terminal domain / SBDS protein, C-terminal domain / Ribosome maturation protein Sdo1/SBDS / Ribosome maturation protein SBDS, conserved site / Ribosome maturation protein SDO1/SBDS, central domain / Ribosome maturation protein Sdo1/SBDS, central domain superfamily / SBDS protein, domain II ...SBDS protein C-terminal domain, subdomain 1 / Hypothetical 12.0 Kda Protein In Nam8-gar1 Intergenic Region; Chain: A; / Ribosome maturation protein SBDS, N-terminal domain / Ribosome maturation protein SDO1/SBDS, C-terminal domain / SBDS protein, C-terminal domain / Ribosome maturation protein Sdo1/SBDS / Ribosome maturation protein SBDS, conserved site / Ribosome maturation protein SDO1/SBDS, central domain / Ribosome maturation protein Sdo1/SBDS, central domain superfamily / SBDS protein, domain II / Uncharacterized protein family UPF0023 signature. / Ribosome maturation protein SDO1/SBDS, N-terminal / Ribosome maturation protein SBDS, N-terminal domain superfamily / Ribosome maturation protein Sdo1/SBDS-like / Shwachman-Bodian-Diamond syndrome (SBDS) protein / Alpha-Beta Plaits - #240 / EF-G domain III/V-like / Arc Repressor Mutant, subunit A / Alpha-Beta Plaits / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Ribosome maturation protein SDO1 homolog / Ribosome maturation protein SDO1 homolog
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMazzorana, M. / Foadi, J. / Siliqi, D. / Sanchez-Puig, N.
Funding support Mexico, Italy, United Kingdom, 3items
OrganizationGrant numberCountry
CONACyT283909 Mexico
Ministero degli Affari Esteri e dalla Cooperazione InternazionalePGR2014-2017 Italy
Diamond Light SourceMX11690-13 United Kingdom
CitationJournal: Crystals / Year: 2018
Title: Conformational flexibility of proteins involved in ribosome biogenesis: investigations via Small Angle X-ray Scattering (SAXS)
Authors: Siliqi, D. / Foadi, J. / Mazzorana, M. / Altamura, D. / Mendez Godoy, A. / Sanchez Puig, N.
History
DepositionFeb 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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

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Assembly

Deposited unit
A: Ribosome maturation protein SDO1-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9092
Polymers26,8031
Non-polymers1061
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint2 kcal/mol
Surface area13080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.810, 44.520, 54.710
Angle α, β, γ (deg.)75.08, 84.52, 69.72
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Ribosome maturation protein SDO1-like protein


Mass: 26803.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: XD40_1041, XD48_1723 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A101DZV9, UniProt: O29759*PLUS
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.78 Å3/Da / Density % sol: 55.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.02M 1,6-Hexanediol; 0.02M 1-Butanol; 0.02M 1,2-Propanediol; 0.02M 2- Propanol; 0.02M 1,4-Butanediol; 0.02M 1,3-Propanediol;0.05 M Imidazole; 0.05 M MES; 12.5% v/v MPD; 12.5% PEG 1000; 12.5% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.73→36.71 Å / Num. obs: 28569 / % possible obs: 94.6 % / Redundancy: 1.8 % / Rsym value: 0.178 / Net I/σ(I): 5.4
Reflection shellResolution: 1.73→1.77 Å / Rsym value: 0.648

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Processing

Software
NameClassification
PHENIXrefinement
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T95

1t95


Resolution: 1.9→36.708 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 26.58
RfactorNum. reflection% reflectionSelection details
Rfree0.2329 1034 4.76 %RANDOM
Rwork0.1967 ---
obs0.1983 21716 95.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→36.708 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1853 0 7 81 1941
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081896
X-RAY DIFFRACTIONf_angle_d0.8242545
X-RAY DIFFRACTIONf_dihedral_angle_d8.1131674
X-RAY DIFFRACTIONf_chiral_restr0.054283
X-RAY DIFFRACTIONf_plane_restr0.005331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.00020.30911430.26992898X-RAY DIFFRACTION94
2.0002-2.12550.2821630.24712892X-RAY DIFFRACTION93
2.1255-2.28960.28331500.25042922X-RAY DIFFRACTION94
2.2896-2.51990.27951400.23182965X-RAY DIFFRACTION96
2.5199-2.88440.28651580.22892973X-RAY DIFFRACTION96
2.8844-3.63360.24851480.21352999X-RAY DIFFRACTION97
3.6336-36.71490.16891320.15223033X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.98370.68060.15251.36370.58740.9449-0.0677-0.09260.2126-0.0336-0.02010.0388-0.0697-0.02210.00010.214-0.00130.01650.3418-0.04360.280315.554211.11377.8944
21.71371.18390.38390.2060.13060.58-0.03190.2508-0.18890.01020.1721-0.1276-0.0810.1892-00.2829-0.0308-0.01230.3426-0.00970.282524.302313.407310.0893
30.76920.321-0.06381.79650.39111.45380.1962-0.2321-0.2385-0.1409-0.01510.18450.233-0.1797-0.00010.3522-0.0224-0.0410.2880.01530.3131.996-3.3123-10.1117
40.1325-0.90071.78311.949-0.16792.1547-0.14760.0566-0.18030.3290.11640.3493-0.1803-0.0810.00120.34060.03850.06140.24130.04960.3473-12.859512.5626-25.1209
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 49 )
2X-RAY DIFFRACTION2chain 'A' and (resid 50 through 90 )
3X-RAY DIFFRACTION3chain 'A' and (resid 91 through 155 )
4X-RAY DIFFRACTION4chain 'A' and (resid 156 through 236 )

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