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- PDB-1rss: RIBOSOMAL PROTEIN S7 FROM THERMUS THERMOPHILUS -

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Basic information

Entry
Database: PDB / ID: 1rss
TitleRIBOSOMAL PROTEIN S7 FROM THERMUS THERMOPHILUS
ComponentsRIBOSOMAL PROTEIN S7
KeywordsRIBOSOMAL PROTEIN / RNA-BINDING / TRANSLATION
Function / homology
Function and homology information


small ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / translation
Similarity search - Function
Ribosomal Protein S7 / Ribosomal protein S7/S5 / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S7, conserved site / Ribosomal protein S7 signature. / Ribosomal protein S5/S7 / Ribosomal protein S7 domain / Ribosomal protein S7 domain superfamily / Ribosomal protein S7p/S5e / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Small ribosomal subunit protein uS7
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsWimberly, B. / White, S. / Ramakrishnan, V.
CitationJournal: Structure / Year: 1997
Title: The structure of ribosomal protein S7 at 1.9 A resolution reveals a beta-hairpin motif that binds double-stranded nucleic acids.
Authors: Wimberly, B.T. / White, S.W. / Ramakrishnan, V.
History
DepositionAug 5, 1997Processing site: BNL
Revision 1.0Feb 11, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RIBOSOMAL PROTEIN S7


Theoretical massNumber of molelcules
Total (without water)17,3511
Polymers17,3511
Non-polymers00
Water2,630146
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.530, 55.530, 103.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein RIBOSOMAL PROTEIN S7


Mass: 17351.115 Da / Num. of mol.: 1 / Mutation: 5 RESIDUES DELETED FROM N-TERMINUS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Cell line: BL21 / Gene: S7 / Plasmid: PET-13A / Species (production host): Escherichia coli / Gene (production host): S7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P17291
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.7 Å3/Da / Density % sol: 40 % / Description: 2 WAVELENGTH MAD EXPERIMENT
Crystal growTemperature: 277 K / pH: 8
Details: CRYSTALLIZED FROM 15% PEG 8000, 20% GLYCEROL, 6% MPD, 0.1 M NAHCO3, 0.1 M TRIS PH 8.0 AT 4 C, temperature 277K
Crystal grow
*PLUS
Temperature: 4-13 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
22.5-5 %MPD1drop
33.5 mg/mlprotein1drop
42.5 mMHEPES1drop
50.05 M1dropNaCl
62.5 mM2-mercaptoethanol1drop
85-10 %MPD1reservoir
1PEG80001drop
7PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.98 / Wavelength: 0.98, 1.01
DetectorType: BRANDEIS / Detector: CCD / Date: May 15, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.981
21.011
ReflectionResolution: 1.9→100 Å / Num. obs: 13428 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.033 / Rsym value: 0.04 / Net I/σ(I): 37
Reflection shellResolution: 1.9→1.98 Å / Redundancy: 5 % / Rmerge(I) obs: 0.064 / Mean I/σ(I) obs: 5 / Rsym value: 0.307 / % possible all: 95
Reflection
*PLUS
Num. measured all: 103923

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Processing

Software
NameVersionClassification
SHARPphasing
X-PLOR3.843model building
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.843phasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→6 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.284 1279 9.9 %RANDOM
Rwork0.229 ---
obs0.229 12890 99.9 %-
Displacement parametersBiso mean: 35.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-6 Å
Luzzati sigma a0.2 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 1.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1127 0 0 130 1257
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.18
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.321.5
X-RAY DIFFRACTIONx_mcangle_it2.22
X-RAY DIFFRACTIONx_scbond_it2.542
X-RAY DIFFRACTIONx_scangle_it4.142.5
LS refinement shellResolution: 1.9→2.01 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.333 220 10.5 %
Rwork0.362 1868 -
obs--99.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.18

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