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- PDB-2bxj: Double Mutant of the Ribosomal Protein S6 -

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Basic information

Entry
Database: PDB / ID: 2bxj
TitleDouble Mutant of the Ribosomal Protein S6
Components30S RIBOSOMAL PROTEIN S6
KeywordsRIBOSOMAL PROTEIN / S6 DOUBLE MUTANT / RNA-BINDING
Function / homology
Function and homology information


rRNA binding / ribosome / structural constituent of 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
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsOtzen, D.E.
Citation
Journal: Protein Eng.Des.Sel. / Year: 2005
Title: Antagonism, Non-Native Interactions and Non-Two-State Folding in S6 Revealed by Double-Mutant Cycle Analysis.
Authors: Otzen, D.E.
#1: Journal: Biochemistry / Year: 1999
Title: Structural Changes in the Transition State of Protein Folding: Alternative Interpretations of Curved Chevron Plots
Authors: Otzen, D.E. / Kristensen, O. / Proctor, M. / Oliveberg, M.
#2: Journal: Biochemistry / Year: 1997
Title: High-Energy Channelling in Protein Folding
Authors: Silow, M. / Oliveberg, M.
#3: 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
DepositionJul 26, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: 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
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 30S RIBOSOMAL PROTEIN S6
B: 30S RIBOSOMAL PROTEIN S6


Theoretical massNumber of molelcules
Total (without water)23,8092
Polymers23,8092
Non-polymers00
Water1,26170
1
A: 30S RIBOSOMAL PROTEIN S6


Theoretical massNumber of molelcules
Total (without water)11,9051
Polymers11,9051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: 30S RIBOSOMAL PROTEIN S6


Theoretical massNumber of molelcules
Total (without water)11,9051
Polymers11,9051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)84.252, 84.252, 144.367
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein 30S RIBOSOMAL PROTEIN S6 /


Mass: 11904.593 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P23370
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LEU 30 TO ALA ENGINEERED RESIDUE IN CHAIN B, LEU 30 TO ALA
Sequence detailsDOUBLE MUTANT OF P23370 (L30A, L75A)

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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: 2.06 Å3/Da / Density % sol: 40.24 %
Crystal growDetails: 0.2M NA-CITRATE, 0.1M TRIS-CL PH 8.5, 25% (V/V) PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→23.05 Å / Num. obs: 12515 / % possible obs: 97 % / Observed criterion σ(I): 3 / Redundancy: 18 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 23.56
Reflection shellResolution: 2.4→2.55 Å / Redundancy: 12 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 6.9 / % possible all: 95.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LOU

1lou


Resolution: 2.4→23.05 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 261301.8 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.236 618 5.1 %RANDOM
Rwork0.198 ---
obs0.198 12080 97 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.8353 Å2 / ksol: 0.321317 e/Å3
Displacement parametersBiso mean: 27.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å23.47 Å20 Å2
2--0.46 Å20 Å2
3----0.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.4→23.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1638 0 0 70 1708
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_d24.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.071.5
X-RAY DIFFRACTIONc_mcangle_it1.762
X-RAY DIFFRACTIONc_scbond_it2.192
X-RAY DIFFRACTIONc_scangle_it3.412.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.294 89 4.6 %
Rwork0.24 1833 -
obs--95.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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