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- PDB-3kbg: Crystal structure of the 30S ribosomal protein S4e from Thermopla... -

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Basic information

Entry
Database: PDB / ID: 3kbg
TitleCrystal structure of the 30S ribosomal protein S4e from Thermoplasma acidophilum. Northeast Structural Genomics Consortium Target TaR28.
Components30S ribosomal protein S4eRibosome
KeywordsRIBOSOMAL PROTEIN / 30S ribosomal protein S4e / rps4e / RS4E_THEAC / TaR28 / NESG / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / Ribonucleoprotein / RNA-binding / rRNA-binding
Function / homology
Function and homology information


rRNA binding / ribosome / structural constituent of ribosome / translation
Similarity search - Function
Ribosomal protein S4, central domain / RNA-binding S4 domain / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / SH3 type barrels. - #30 / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e / SH3 type barrels. ...Ribosomal protein S4, central domain / RNA-binding S4 domain / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / SH3 type barrels. - #30 / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e / SH3 type barrels. / S4 RNA-binding domain / RNA-binding S4 domain / S4 domain / S4 RNA-binding domain profile. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Ribosomal protein L2, domain 2 / Roll / Roll / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
30S ribosomal protein S4e
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsVorobiev, S.M. / Su, M. / Seetharaman, J. / Belote, R.L. / Ciccosanti, C. / Patel, D. / Liu, J. / Rost, B. / Acton, T.B. / Xiao, R. ...Vorobiev, S.M. / Su, M. / Seetharaman, J. / Belote, R.L. / Ciccosanti, C. / Patel, D. / Liu, J. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the 30S ribosomal protein S4e from Thermoplasma acidophilum.
Authors: Vorobiev, S.M. / Su, M. / Seetharaman, J. / Belote, R.L. / Ciccosanti, C. / Liu, J. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionOct 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 30S ribosomal protein S4e


Theoretical massNumber of molelcules
Total (without water)24,0851
Polymers24,0851
Non-polymers00
Water3,477193
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: 30S ribosomal protein S4e

A: 30S ribosomal protein S4e


Theoretical massNumber of molelcules
Total (without water)48,1692
Polymers48,1692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+1/31
Buried area1910 Å2
ΔGint-9 kcal/mol
Surface area18790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.831, 74.831, 64.133
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-597-

HOH

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Components

#1: Protein 30S ribosomal protein S4e / Ribosome


Mass: 24084.703 Da / Num. of mol.: 1 / Mutation: K148I, W154L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: rps4e, Ta1259 / Plasmid: pET 21-23C / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q56230
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.15 Å3/Da / Density % sol: 42.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 3350, 0.2M NaF, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97912 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 40542 / Num. obs: 40501 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 77.2
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 9.3 / Num. unique all: 2035 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SnBphasing
RESOLVEmodel building
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.75→28.921 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2172 2080 5.15 %RANDOM
Rwork0.1844 ---
obs0.1861 40427 99.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.632 Å2 / ksol: 0.351 e/Å3
Refinement stepCycle: LAST / Resolution: 1.75→28.921 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1473 0 0 193 1666
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161493
X-RAY DIFFRACTIONf_angle_d1.5322007
X-RAY DIFFRACTIONf_dihedral_angle_d14.392558
X-RAY DIFFRACTIONf_chiral_restr0.11238
X-RAY DIFFRACTIONf_plane_restr0.007253
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.79070.23991280.2072565X-RAY DIFFRACTION99
1.7907-1.83550.25051360.20632521X-RAY DIFFRACTION100
1.8355-1.88510.24281330.20912573X-RAY DIFFRACTION100
1.8851-1.94060.25011260.19512573X-RAY DIFFRACTION100
1.9406-2.00320.23531680.18752553X-RAY DIFFRACTION100
2.0032-2.07480.20831360.17722521X-RAY DIFFRACTION100
2.0748-2.15780.25651240.18282582X-RAY DIFFRACTION100
2.1578-2.2560.16521250.17552581X-RAY DIFFRACTION100
2.256-2.37490.22261510.16852530X-RAY DIFFRACTION100
2.3749-2.52360.1881370.18342584X-RAY DIFFRACTION100
2.5236-2.71830.20251570.18292532X-RAY DIFFRACTION100
2.7183-2.99160.19351690.19572565X-RAY DIFFRACTION100
2.9916-3.42390.28181170.18632565X-RAY DIFFRACTION100
3.4239-4.31150.21631580.1652553X-RAY DIFFRACTION100
4.3115-28.92490.18631150.17962549X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 24.7777 Å / Origin y: 44.7101 Å / Origin z: 13.0267 Å
111213212223313233
T0.1423 Å2-0.0093 Å2-0.0136 Å2-0.0394 Å20.0172 Å2--0.0826 Å2
L0.5288 °20.0674 °20.0759 °2-0.3133 °20.0969 °2--0.484 °2
S-0.0051 Å °-0.018 Å °-0.0912 Å °0.1561 Å °0.0248 Å °-0.0062 Å °-0.0397 Å °-0.0121 Å °-0.0139 Å °
Refinement TLS groupSelection details: chain A

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