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- PDB-1iqv: Crystal Structure Analysis of the archaebacterial ribosomal protein S7 -

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Basic information

Entry
Database: PDB / ID: 1iqv
TitleCrystal Structure Analysis of the archaebacterial ribosomal protein S7
ComponentsRIBOSOMAL PROTEIN S7
KeywordsRIBOSOME / RIBOSOMAL PROTEIN / RNA-BINDING / DECODING CENTER / HELIX-TURN-HELIX
Function / homology
Function and homology information


small ribosomal subunit / rRNA binding / structural constituent of ribosome / translation
Similarity search - Function
Ribosomal protein S7, archaeal / Ribosomal Protein S7 / Ribosomal protein S7/S5 / Ribosomal protein S5/S7, eukaryotic/archaeal / 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
30S ribosomal protein S7
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHosaka, H. / Yao, M. / Kimura, M. / Tanaka, I.
CitationJournal: J.Biochem. / Year: 2001
Title: The structure of the archaebacterial ribosomal protein S7 and its possible interaction with 16S rRNA.
Authors: Hosaka, H. / Yao, M. / Kimura, M. / Tanaka, I.
History
DepositionAug 7, 2001Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 29, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI
Revision 1.4Oct 25, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RIBOSOMAL PROTEIN S7


Theoretical massNumber of molelcules
Total (without water)25,0291
Polymers25,0291
Non-polymers00
Water2,360131
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.9, 58.9, 118.1
Angle α, β, γ (deg.)90, 90, 120
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein RIBOSOMAL PROTEIN S7 / 30S RIBOSOMAL PROTEIN S7P


Mass: 25029.232 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: PH1541 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: O59230
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.1 Å3/Da / Density % sol: 41.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG3000, sodium chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11 mMdithiothreitol1drop
210 mMprotein1drop
30.1 MTris-HCl1reservoirpH7.0
40.2 M1reservoirNaCl
530 %(w/v)PEG30001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: OXFORD PX210 / Detector: CCD / Date: Mar 14, 2001
RadiationMonochromator: Monochromator + Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.1→31 Å / Num. all: 14407 / Num. obs: 14407 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.7 % / Biso Wilson estimate: 41.4 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.077 / Net I/σ(I): 7.2
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.262 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2048 / Rsym value: 0.243 / % possible all: 99.8
Reflection
*PLUS
Lowest resolution: 40 Å / Num. measured all: 139697
Reflection shell
*PLUS
% possible obs: 99.8 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HUS

1hus


Resolution: 2.1→10 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1420 10.14 %RANDOM
Rwork0.196 ---
all-14407 --
obs-13999 98.2 %-
Solvent computationBsol: 66.8 Å2 / ksol: 0.436 e/Å3
Displacement parametersBiso mean: 35.7 Å2
Baniso -1Baniso -2Baniso -3
1--3.542 Å2-2.812 Å20 Å2
2---3.542 Å20 Å2
3---7.084 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1318 0 0 131 1449
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.03
X-RAY DIFFRACTIONc_bond_d0.0049
X-RAY DIFFRACTIONc_dihedral_angle_d19.56
X-RAY DIFFRACTIONc_improper_angle_d0.767
X-RAY DIFFRACTIONc_mcbond_it1.757
X-RAY DIFFRACTIONc_mcangle_it2.732
X-RAY DIFFRACTIONc_scbond_it2.948
X-RAY DIFFRACTIONc_scangle_it4.292
LS refinement shellResolution: 2.1→2.17 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.265 138 10 %
Rwork0.243 1213 -
obs-1351 96.6 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 10 Å / Num. reflection obs: 14240 / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.196 / Rfactor Rfree: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 35.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.56
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.767
LS refinement shell
*PLUS
Rfactor Rfree: 0.265 / % reflection Rfree: 10 % / Rfactor Rwork: 0.243

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