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- PDB-2dyi: Crystal structure of 16S ribosomal RNA processing protein RimM fr... -

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Basic information

Entry
Database: PDB / ID: 2dyi
TitleCrystal structure of 16S ribosomal RNA processing protein RimM from Thermus thermophilus HB8
ComponentsProbable 16S rRNA-processing protein rimM
KeywordsRIBOSOME / ribosomal protein S19 / 16S rRNA processing / PRC-barrel / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


rRNA processing / ribosome binding / ribosomal small subunit biogenesis / ribosome / cytoplasm
Similarity search - Function
RimM / PRC-barrel domain / RimM, N-terminal / 16S rRNA processing protein RimM / RimM, N-terminal domain superfamily / RimM N-terminal domain / PRC-barrel domain / PRC-barrel domain / PRC-barrel-like superfamily / Elongation Factor Tu (Ef-tu); domain 3 ...RimM / PRC-barrel domain / RimM, N-terminal / 16S rRNA processing protein RimM / RimM, N-terminal domain superfamily / RimM N-terminal domain / PRC-barrel domain / PRC-barrel domain / PRC-barrel-like superfamily / Elongation Factor Tu (Ef-tu); domain 3 / SH3 type barrels. / Translation protein, beta-barrel domain superfamily / Roll / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Ribosome maturation factor RimM
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKawazoe, M. / Takemoto, C. / Kaminishi, T. / Tatsuguchi, A. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be published
Title: Crystal structure of 16S ribosomal RNA processing protein RimM from Thermus thermophilus HB8
Authors: Kawazoe, M. / Takemoto, C. / Kaminishi, T. / Tatsuguchi, A. / Shirouzu, M. / Yokoyama, S.
History
DepositionSep 14, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 14, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable 16S rRNA-processing protein rimM


Theoretical massNumber of molelcules
Total (without water)18,0951
Polymers18,0951
Non-polymers00
Water2,468137
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.328, 53.103, 70.437
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 Probable 16S rRNA-processing protein rimM


Mass: 18094.768 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA1033 / Plasmid: pET11b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SJH5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.65 Å3/Da / Density % sol: 53.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 25mM Tris-HCl, 0.025% w/v Polyethylene glycol 6000, 0.5M Lithium sulfate, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 15, 2005 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→42.4 Å / Num. obs: 13576 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.17 % / Biso Wilson estimate: 6.9 Å2 / Rsym value: 0.083 / Net I/σ(I): 23.8
Reflection shellResolution: 2→2.07 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 6.93 / Num. unique all: 1316 / Rsym value: 0.314 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
DENZOdata reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Preliminary assigned NMR model

Resolution: 2→42.4 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1166587.98 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.256 654 4.8 %RANDOM
Rwork0.192 ---
obs0.192 13529 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.9156 Å2 / ksol: 0.374585 e/Å3
Displacement parametersBiso mean: 23.3 Å2
Baniso -1Baniso -2Baniso -3
1--3.28 Å20 Å20 Å2
2--4.27 Å20 Å2
3----0.99 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 2→42.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1280 0 0 137 1417
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.022
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_deg2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.28
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.091.5
X-RAY DIFFRACTIONc_mcangle_it2.772
X-RAY DIFFRACTIONc_scbond_it3.452
X-RAY DIFFRACTIONc_scangle_it5.032.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.265 106 4.8 %
Rwork0.194 2102 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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