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- PDB-3ra6: Crystal structure of T. celer L30e E62A/K46A variant -

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Basic information

Entry
Database: PDB / ID: 3ra6
TitleCrystal structure of T. celer L30e E62A/K46A variant
Components50S ribosomal protein L30e
KeywordsRIBOSOMAL PROTEIN / L30e / Thermophilic / globular protein
Function / homology
Function and homology information


cytosolic large ribosomal subunit / structural constituent of ribosome / translation / RNA binding
Similarity search - Function
Ribosomal protein L30/S12 / Ribosomal protein L30e / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L30e signature 1. / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / Ribosomal protein L30/YlxQ / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like ...Ribosomal protein L30/S12 / Ribosomal protein L30e / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L30e signature 1. / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / Ribosomal protein L30/YlxQ / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Large ribosomal subunit protein eL30
Similarity search - Component
Biological speciesThermococcus celer (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChan, C.H. / Yu, T.H. / Wong, K.B.
CitationJournal: Plos One / Year: 2011
Title: Stabilizing salt-bridge enhances protein thermostability by reducing the heat capacity change of unfolding
Authors: Chan, C.H. / Yu, T.H. / Wong, K.B.
History
DepositionMar 27, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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: 50S ribosomal protein L30e


Theoretical massNumber of molelcules
Total (without water)10,8661
Polymers10,8661
Non-polymers00
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)23.587, 53.913, 34.298
Angle α, β, γ (deg.)90.00, 109.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 50S ribosomal protein L30e


Mass: 10865.570 Da / Num. of mol.: 1 / Mutation: E62A, K46A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus celer (archaea) / Gene: rpl30e / Plasmid: PET3C / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: P29160
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 1.9 Å3/Da / Density % sol: 35.12 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 5% PEG MME 2000, 0.1M MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 15, 2009 / Details: mirrors
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→32.398 Å / Num. obs: 5520 / % possible obs: 100 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 / Redundancy: 2.8 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 15.2
Reflection shellResolution: 2→2.11 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.174 / Mean I/σ(I) obs: 4.8 / Num. unique all: 791 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H7M

1h7m


Resolution: 2→32.398 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.27 / σ(F): 1.41 / Phase error: 27.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2532 537 9.81 %RANDOM
Rwork0.196 ---
all0.2016 5473 --
obs0.2016 5473 98.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.407 Å2 / ksol: 0.395 e/Å3
Displacement parametersBiso max: 50.61 Å2 / Biso mean: 23.2088 Å2 / Biso min: 9.06 Å2
Baniso -1Baniso -2Baniso -3
1-3.0031 Å2-0 Å2-3.6507 Å2
2---5.3822 Å2-0 Å2
3---2.3791 Å2
Refinement stepCycle: LAST / Resolution: 2→32.398 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms733 0 0 83 816
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007744
X-RAY DIFFRACTIONf_angle_d1.0081005
X-RAY DIFFRACTIONf_chiral_restr0.061117
X-RAY DIFFRACTIONf_plane_restr0.004129
X-RAY DIFFRACTIONf_dihedral_angle_d13.442274
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0001-2.20130.28991290.217612331362100
2.2013-2.51980.37811340.25611204133898
2.5198-3.17420.24481370.20612521389100
3.1742-32.40240.18781370.16081247138498

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