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- PDB-4iyl: 30S ribosomal protein S15 from Campylobacter jejuni -

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Basic information

Entry
Database: PDB / ID: 4iyl
Title30S ribosomal protein S15 from Campylobacter jejuni
Components30S ribosomal protein S15
KeywordsRIBOSOMAL PROTEIN / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID / rRNA binding / translation / NIAID / National Institute of Allergy and Infectious Diseases
Function / homology
Function and homology information


cytosolic small ribosomal subunit / rRNA binding / structural constituent of ribosome / translation
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3130 / S15/NS1, RNA-binding / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Ribosomal protein S15, bacterial-type / Helix Hairpins / Ribosomal protein S15 signature. / Ribosomal protein S15 / Ribosomal_S15 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3130 / S15/NS1, RNA-binding / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Ribosomal protein S15, bacterial-type / Helix Hairpins / Ribosomal protein S15 signature. / Ribosomal protein S15 / Ribosomal_S15 / Ribosomal protein S15 / S15/NS1, RNA-binding / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Small ribosomal subunit protein uS15
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsOsipiuk, J. / Nocek, B. / Gu, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 30S ribosomal protein S15 from Campylobacter jejuni
Authors: Osipiuk, J. / Nocek, B. / Gu, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A.
History
DepositionJan 28, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 6, 2013ID: 3ULW
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 30S ribosomal protein S15


Theoretical massNumber of molelcules
Total (without water)10,5191
Polymers10,5191
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: 30S ribosomal protein S15

A: 30S ribosomal protein S15


Theoretical massNumber of molelcules
Total (without water)21,0392
Polymers21,0392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+11
Buried area3230 Å2
ΔGint-33 kcal/mol
Surface area11650 Å2
MethodPISA
3
A: 30S ribosomal protein S15

A: 30S ribosomal protein S15

A: 30S ribosomal protein S15

A: 30S ribosomal protein S15


Theoretical massNumber of molelcules
Total (without water)42,0774
Polymers42,0774
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area8540 Å2
ΔGint-76 kcal/mol
Surface area21220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.239, 58.626, 115.874
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Detailsbiological unit is the same as asymmetric unit, based on ribosome structure

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Components

#1: Protein 30S ribosomal protein S15


Mass: 10519.337 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni (Campylobacter)
Strain: NCTC 11168 / Gene: Cj0884, rpsO / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q0PA13
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.49 Å3/Da / Density % sol: 64.76 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: 0.49 M sodium phosphate, 0.91 M di-potassium phosphate, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 25, 2010
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.36→32.3 Å / Num. all: 5992 / Num. obs: 5992 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 68.7 Å2 / Rmerge(I) obs: 0.098 / Χ2: 1.39 / Net I/σ(I): 10.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.38-2.422.50.5872.022650.95188.3
2.42-2.472.70.6052901.09195.4
2.47-2.512.80.6123031.01397.4
2.51-2.563.10.6193010.95795.6
2.56-2.623.20.4752911.11198.6
2.62-2.683.40.4353011.10799
2.68-2.753.70.4423111.04196
2.75-2.823.70.3873051.26499.7
2.82-2.94.10.3192951.1695.5
2.9-340.33061.26199.7
3-3.1140.2193081.39995.7
3.11-3.234.10.1992941.37298.7
3.23-3.3840.1543041.55495.3
3.38-3.5540.1173041.70998.7
3.55-3.7840.0853021.64395.6
3.78-4.073.90.0783121.69395.7
4.07-4.483.70.0623041.52995.6
4.48-5.133.50.0673021.895.9
5.13-6.463.60.0783081.78393.1
6.46-503.10.0682861.80578.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y0Y

2y0y
PDB Unreleased entry


Resolution: 2.36→32.27 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 1 / SU B: 9.575 / SU ML: 0.197 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.287 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2809 278 4.6 %RANDOM
Rwork0.2458 ---
all0.2474 5992 --
obs0.2474 5992 94.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 151.27 Å2 / Biso mean: 81.4788 Å2 / Biso min: 45.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.64 Å20 Å20 Å2
2---5.48 Å20 Å2
3---3.84 Å2
Refinement stepCycle: LAST / Resolution: 2.36→32.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms678 0 0 4 682
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONf_bond_refined_d0.0120.019685
X-RAY DIFFRACTIONf_bond_other_d0.0010.02725
X-RAY DIFFRACTIONf_angle_refined_deg1.6112.016915
X-RAY DIFFRACTIONf_angle_other_deg0.77131672
X-RAY DIFFRACTIONf_dihedral_angle_1_deg6.362584
X-RAY DIFFRACTIONf_dihedral_angle_2_deg34.97423.225
X-RAY DIFFRACTIONf_dihedral_angle_3_deg20.5215148
X-RAY DIFFRACTIONf_dihedral_angle_4_deg11.195155
X-RAY DIFFRACTIONf_chiral_restr0.070.2109
X-RAY DIFFRACTIONf_gen_planes_refined0.0050.02726
X-RAY DIFFRACTIONf_gen_planes_other0.0010.02141
LS refinement shellResolution: 2.362→2.423 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 15 -
Rwork0.358 351 -
all-366 -
obs-366 79.39 %

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