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- PDB-1kuq: CRYSTAL STRUCTURE OF T3C MUTANT S15 RIBOSOMAL PROTEIN IN COMPLEX ... -

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Basic information

Entry
Database: PDB / ID: 1kuq
TitleCRYSTAL STRUCTURE OF T3C MUTANT S15 RIBOSOMAL PROTEIN IN COMPLEX WITH 16S RRNA
Components
  • 16S RIBOSOMAL RNA FRAGMENT
  • 30S RIBOSOMAL PROTEIN S15
KeywordsRIBOSOME / rRNA-protein complex
Function / homology
Function and homology information


rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / cytoplasm
Similarity search - Function
S15/NS1, RNA-binding / Ribosomal protein S15, bacterial-type / Ribosomal_S15 / Ribosomal protein S15 signature. / Ribosomal protein S15 / Ribosomal protein S15 / S15/NS1, RNA-binding / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
RNA / RNA (> 10) / Small ribosomal subunit protein uS15
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsNikulin, A.D. / Tishchenko, S. / Revtovich, S. / Ehresmann, B. / Ehresmann, C. / Dumas, P. / Garber, M. / Nikonov, S. / Nevskaya, N.
Citation
Journal: Biochemistry Mosc. / Year: 2004
Title: Role of N-terminal helix in interaction of ribosomal protein S15 with 16S rRNA.
Authors: Revtovich, S.V. / Nikulin, A.D. / Nikonov, S.V.
History
DepositionJan 22, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 16S RIBOSOMAL RNA FRAGMENT
A: 30S RIBOSOMAL PROTEIN S15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9273
Polymers28,8312
Non-polymers961
Water1086
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.229, 128.229, 64.951
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: RNA chain 16S RIBOSOMAL RNA FRAGMENT


Mass: 18464.963 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): DH1
#2: Protein 30S RIBOSOMAL PROTEIN S15 /


Mass: 10366.200 Da / Num. of mol.: 1 / Mutation: T3C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P80378
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.67 Å3/Da / Density % sol: 53.98 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: ammonium sulphate, KCl, MgCl2, sodium cacodylate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1ammonium sulphate11
2KCl11
3MgCl211
4sodium cacodylate11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 21, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.84→25 Å / Num. all: 7828 / Num. obs: 7828 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 117.9 Å2 / Rmerge(I) obs: 0.049
Reflection shellResolution: 2.84→2.92 Å / Rmerge(I) obs: 0.12 / % possible all: 99.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1DK1

1dk1


Resolution: 2.84→24.41 Å / Rfactor Rfree error: 0.016 / Data cutoff high absF: 1157536.51 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.322 412 5.3 %RANDOM
Rwork0.231 ---
obs0.231 7724 98.8 %-
all-7780 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 69.8947 Å2 / ksol: 0.362129 e/Å3
Displacement parametersBiso mean: 56.9 Å2
Baniso -1Baniso -2Baniso -3
1--4.18 Å24.29 Å20 Å2
2---4.18 Å20 Å2
3---8.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.61 Å0.4 Å
Luzzati d res low-50 Å
Luzzati sigma a0.41 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.84→24.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms703 1292 5 6 2006
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.4
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it9.331.5
X-RAY DIFFRACTIONc_mcangle_it14.42
X-RAY DIFFRACTIONc_scbond_it8.012
X-RAY DIFFRACTIONc_scangle_it10.732.5
LS refinement shellResolution: 2.84→3.02 Å / Rfactor Rfree error: 0.06 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.43 51 4.2 %
Rwork0.376 1161 -
obs--96.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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