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- PDB-3zzp: Circular permutant of ribosomal protein S6, lacking edge strand b... -

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Basic information

Entry
Database: PDB / ID: 3zzp
TitleCircular permutant of ribosomal protein S6, lacking edge strand beta- 2 of wild-type S6.
ComponentsRIBOSOMAL PROTEIN S6
KeywordsRIBOSOMAL PROTEIN / PROTEIN FOLDING / RNA-BINDING
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 / Small ribosomal subunit protein bS6
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.96 Å
AuthorsSaraboji, K. / Haglund, E. / Lindberg, M.O. / Oliveberg, M. / Logan, D.T.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Trimming Down a Protein Structure to its Bare Foldons: Spatial Organization of the Cooperative Unit.
Authors: Haglund, E. / Danielsson, J. / Kadhirvel, S. / Lindberg, M.O. / Logan, D.T. / Oliveberg, M.
History
DepositionSep 2, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 1.4Dec 20, 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: RIBOSOMAL PROTEIN S6


Theoretical massNumber of molelcules
Total (without water)9,0311
Polymers9,0311
Non-polymers00
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)22.200, 40.800, 68.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RIBOSOMAL PROTEIN S6 / TS9


Mass: 9031.086 Da / Num. of mol.: 1 / Fragment: RESIDUES 3-35,55-93
Source method: isolated from a genetically manipulated source
Details: CIRCULAR PERMUTANT OF THE RIBOSOMAL PROTEIN S6 FROM THERMUS THERMOPHILUS, WHICH HAS A LINKER BETWEEN THE WILD-TYPE N-AND C-TERMINI AND AN INCISION BETWEEN K54 AND D55 WITHOUT THE EDGE STRAND ...Details: CIRCULAR PERMUTANT OF THE RIBOSOMAL PROTEIN S6 FROM THERMUS THERMOPHILUS, WHICH HAS A LINKER BETWEEN THE WILD-TYPE N-AND C-TERMINI AND AN INCISION BETWEEN K54 AND D55 WITHOUT THE EDGE STRAND BETA-2 OF WILD-TYPE S6. (RESIDUES 36-54).
Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P23370, UniProt: Q5SLP8*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCIRCULAR PERMUTANT OF THE RIBOSOMAL PROTEIN S6, WHICH HAS A LINKER BETWEEN THE WILD-TYPE N- AND C- ...CIRCULAR PERMUTANT OF THE RIBOSOMAL PROTEIN S6, WHICH HAS A LINKER BETWEEN THE WILD-TYPE N- AND C-TERMINI AND AN INCISION BETWEEN K54 AND D55 WITHOUT THE STRAND BETA-2 OF WILD-TYPE S6 (RESIDUES 36-54).

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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: 1.56 Å3/Da / Density % sol: 20.9 % / Description: NONE
Crystal growpH: 6.5
Details: 1.9M AMMONIUM SULPHATE, 0.1M MES PH 6.5, 8% 1,4 DIOXANE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.038
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 13, 2009
RadiationMonochromator: BENT SI (111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.038 Å / Relative weight: 1
ReflectionResolution: 0.96→20 Å / Num. obs: 38300 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 16
Reflection shellResolution: 0.96→0.99 Å / Redundancy: 4.86 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 3 / % possible all: 98.2

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Processing

Software
NameClassification
SHELXL-97refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RIS

1ris


Resolution: 0.96→20 Å / Num. parameters: 6866 / Num. restraintsaints: 8147 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1369 1932 5 %RANDOM
all0.1129 38148 --
obs0.1129 -99.3 %-
Refine analyzeNum. disordered residues: 9 / Occupancy sum hydrogen: 542.32 / Occupancy sum non hydrogen: 733.74
Refinement stepCycle: LAST / Resolution: 0.96→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms606 0 0 129 735
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d0.033
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0215
X-RAY DIFFRACTIONs_zero_chiral_vol0.094
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.106
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.112
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.007
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.044
X-RAY DIFFRACTIONs_approx_iso_adps0.11

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