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- PDB-1cqm: PROTEIN AGGREGATION AND ALZHEIMER'S DISEASE: CRYSTALLOGRAPHIC ANA... -

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Basic information

Entry
Database: PDB / ID: 1cqm
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.
ComponentsRIBOSOMAL PROTEIN S6
KeywordsRIBOSOMAL PROTEIN / ALZHEIMER DISEASE / RIBOSOMAL PROTEIN S6 / OLIGOMERIZATION
Function / homology
Function and homology information


small ribosomal subunit rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / cytoplasm
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 / Small ribosomal subunit protein bS6
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.65 Å
AuthorsKristensen, O. / Otzen, D.E. / Oliveberg, M.
Citation
Journal: Proc.Natl.Acad.Sci.USA / 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
DepositionAug 8, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary
Revision 1.4Jan 31, 2018Group: Data collection / Experimental preparation / Category: diffrn_source / exptl_crystal_grow
Item: _diffrn_source.pdbx_synchrotron_site / _exptl_crystal_grow.temp
Revision 1.5Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RIBOSOMAL PROTEIN S6
B: RIBOSOMAL PROTEIN S6


Theoretical massNumber of molelcules
Total (without water)23,8302
Polymers23,8302
Non-polymers00
Water2,810156
1
A: RIBOSOMAL PROTEIN S6


Theoretical massNumber of molelcules
Total (without water)11,9151
Polymers11,9151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RIBOSOMAL PROTEIN S6


Theoretical massNumber of molelcules
Total (without water)11,9151
Polymers11,9151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.081, 105.546, 80.838
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein RIBOSOMAL PROTEIN S6


Mass: 11914.761 Da / Num. of mol.: 2 / Mutation: E41A, E42I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P23370, UniProt: Q5SLP8*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.29 Å3/Da / Density % sol: 46.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG 400, SODIUM CITRATE, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 20K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.2 Msodium citrate11
20.1 MTris11pH8.5
330 %PEG40011
46-8 mg/mlprotein11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.0158
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 6, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0158 Å / Relative weight: 1
ReflectionResolution: 1.65→20 Å / Num. all: 25338 / Num. obs: 24926 / % possible obs: 94.6 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 21.6
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.243 / % possible all: 94.6

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Processing

Software
NameVersionClassification
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementResolution: 1.65→20 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1633216.03 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.253 896 3.6 %RANDOM
Rwork0.247 ---
obs0.247 24922 93.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.1 Å2 / ksol: 0.482 e/Å3
Displacement parametersBiso mean: 16.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å20 Å20 Å2
2---1.09 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1638 0 0 156 1794
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.41.5
X-RAY DIFFRACTIONc_mcangle_it0.722
X-RAY DIFFRACTIONc_scbond_it0.692
X-RAY DIFFRACTIONc_scangle_it1.122.5
LS refinement shellResolution: 1.65→1.75 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.304 150 3.7 %
Rwork0.296 3859 -
obs--91.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER_REP.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 3.6 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 16.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.75
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.304 / % reflection Rfree: 3.7 % / Rfactor Rwork: 0.296

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