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- PDB-1gd8: THE CRYSTAL STRUCTURE OF BACTERIA-SPECIFIC L17 RIBOSOMAL PROTEIN. -

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Basic information

Entry
Database: PDB / ID: 1gd8
TitleTHE CRYSTAL STRUCTURE OF BACTERIA-SPECIFIC L17 RIBOSOMAL PROTEIN.
Components50S RIBOSOMAL PROTEIN L17
KeywordsRIBOSOME / TWO DOMAINS / RIBOSOMAL PROTEIN S8-LIKE DOMAIN / TRP REPRESSOR-LIKE DOMAIN / HELIX-TURN-HELIX MOTIF / TWO TYPES OF DIMERS / FOUR DIMERS OF EACH TYPE. / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


cytosolic large ribosomal subunit / structural constituent of ribosome / translation
Similarity search - Function
Ribosomal protein L17 / 50s Ribosomal Protein L17; Chain: A, / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Large ribosomal subunit protein bL17
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsVassylyev, D.G. / Shirouzu, M. / Wada, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: The crystal structure of the bacteria-specific L17 ribosomal protein from Thermus thermophilus.
Authors: Vassylyev, D.G. / Shirouzu, M. / Wada, T. / Yokoyama, S.
History
DepositionSep 22, 2000Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 22, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: 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

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Assembly

Deposited unit
A: 50S RIBOSOMAL PROTEIN L17
B: 50S RIBOSOMAL PROTEIN L17
C: 50S RIBOSOMAL PROTEIN L17
D: 50S RIBOSOMAL PROTEIN L17
E: 50S RIBOSOMAL PROTEIN L17
F: 50S RIBOSOMAL PROTEIN L17
G: 50S RIBOSOMAL PROTEIN L17
H: 50S RIBOSOMAL PROTEIN L17
I: 50S RIBOSOMAL PROTEIN L17


Theoretical massNumber of molelcules
Total (without water)123,7519
Polymers123,7519
Non-polymers00
Water2,828157
1
A: 50S RIBOSOMAL PROTEIN L17


Theoretical massNumber of molelcules
Total (without water)13,7501
Polymers13,7501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 50S RIBOSOMAL PROTEIN L17


Theoretical massNumber of molelcules
Total (without water)13,7501
Polymers13,7501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 50S RIBOSOMAL PROTEIN L17


Theoretical massNumber of molelcules
Total (without water)13,7501
Polymers13,7501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 50S RIBOSOMAL PROTEIN L17


Theoretical massNumber of molelcules
Total (without water)13,7501
Polymers13,7501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: 50S RIBOSOMAL PROTEIN L17


Theoretical massNumber of molelcules
Total (without water)13,7501
Polymers13,7501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: 50S RIBOSOMAL PROTEIN L17


Theoretical massNumber of molelcules
Total (without water)13,7501
Polymers13,7501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: 50S RIBOSOMAL PROTEIN L17


Theoretical massNumber of molelcules
Total (without water)13,7501
Polymers13,7501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: 50S RIBOSOMAL PROTEIN L17


Theoretical massNumber of molelcules
Total (without water)13,7501
Polymers13,7501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: 50S RIBOSOMAL PROTEIN L17


Theoretical massNumber of molelcules
Total (without water)13,7501
Polymers13,7501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.239, 109.239, 128.841
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein
50S RIBOSOMAL PROTEIN L17 /


Mass: 13750.148 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: PET11 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Z9H5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 3.11 Å3/Da / Density % sol: 60.39 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: PEG MME 5000, Lithium sulphate, Sodium chloride, Methanol, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 303K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 67043 / Num. obs: 63819 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 45 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 11.7
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4 % / Rmerge(I) obs: 0.245 / Num. unique all: 5825 / % possible all: 86.8

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.3→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: The refinement was performed using the merohedral twinning fraction of 0.347.
RfactorNum. reflection% reflectionSelection details
Rfree0.254 3065 4.8026 %THIN SHELLS FOR TWINNED CRYSTAL DATA
Rwork0.21 ---
all0.213 67043 --
obs0.213 63819 95.2 %-
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7695 0 0 157 7852
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.32
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_torsion_deg21.26
X-RAY DIFFRACTIONc_torsion_impr_deg0.799

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