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- PDB-1qjh: Protein Aggregation and Alzheimer's Disease: Crystallographic Ana... -

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Basic information

Entry
Database: PDB / ID: 1qjh
TitleProtein Aggregation and Alzheimer's Disease: Crystallographic Analysis of the Phenomenon. Engineered version of the ribosomal protein S6 used as a stable scaffold to study oligomerization.
Components30S ribosomal protein S6
KeywordsRIBOSOMAL PROTEIN / ALZHEIMER DISEASE / RIBOSOMAL PROTEIN S6 / OLIGOMERIZATION
Function / homology
Function and homology information


small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / structural constituent of ribosome / translation
Similarity search - Function
Ribosomal protein S6/Translation elongation factor EF1B / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Translation elongation factor EF1B/ribosomal protein S6 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Small ribosomal subunit protein bS6
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKristensen, O. / Otzen, D.E. / Oliveberg, M.
Citation
Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2000
Title: Designed protein tetramer zipped together with a hydrophobic Alzheimer homology: a structural clue to amyloid assembly.
Authors: Otzen, D.E. / Kristensen, O. / Oliveberg, M.
#1: Journal: Embo J. / Year: 1994
Title: Crystal Structure of the Ribosomal Protein S6 from Thermus Thermophilus
Authors: Lindahl, M. / Svensson, L.A. / Liljas, A. / Sedelnikova, S.E. / Eliseikina, I.A. / Fomenkova, N.P. / Nevskaya, N. / Nikonov, S.V. / Garber, M.B. / Muranova, T.A. / Rykonova, A.I. / Amons, R.
History
DepositionJun 24, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 29, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 12, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / entity_name_com / entity_src_gen / pdbx_entity_src_syn / struct_ref
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity.pdbx_description / _entity.src_method / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 30S ribosomal protein S6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8552
Polymers11,8311
Non-polymers241
Water81145
1
A: 30S ribosomal protein S6
hetero molecules

A: 30S ribosomal protein S6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7104
Polymers23,6612
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area1710 Å2
ΔGint-18 kcal/mol
Surface area12180 Å2
MethodPQS
Unit cell
Length a, b, c (Å)49.701, 49.701, 73.255
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-1000-

MG

21A-2003-

HOH

31A-2023-

HOH

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Components

#1: Protein 30S ribosomal protein S6 / TS9


Mass: 11830.700 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: rpsF, rps6 / Production host: Escherichia coli (E. coli) / References: UniProt: P23370
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 1.9 Å3/Da / Density % sol: 35 %
Crystal growpH: 7 / Details: pH 7.00
Crystal
*PLUS
Crystal grow
*PLUS
Method: unknown / pH: 8.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.2 Msodium citrate11
20.1 MTris11pH8.5
320 %PEG40011
46-8 mg/mlprotein11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.995
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 1999 / Details: BENDABLE MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.995 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 5041 / % possible obs: 99.8 % / Redundancy: 11.6 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 35
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 11.6 % / Rmerge(I) obs: 0.226 / Mean I/σ(I) obs: 11 / Rsym value: 0.226 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RIS

1ris


Resolution: 2.2→35 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 2132615.58 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.275 497 9.9 %RANDOM
Rwork0.205 ---
obs0.205 5038 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.2756 Å2 / ksol: 0.384563 e/Å3
Displacement parametersBiso mean: 34.7 Å2
Baniso -1Baniso -2Baniso -3
1-2.55 Å20 Å20 Å2
2--2.55 Å20 Å2
3----5.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2.2→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms768 0 1 45 814
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.306 82 10.1 %
Rwork0.216 732 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76

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