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- PDB-3ra5: Crystal structure of T. celer L30e E6A/R92A variant -

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Basic information

Entry
Database: PDB / ID: 3ra5
TitleCrystal structure of T. celer L30e E6A/R92A variant
Components50S ribosomal protein L30eRibosome
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 / Ribosomal protein L30e, conserved site / Ribosomal protein L30/YlxQ / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L30e signature 1. / Ribosomal protein L30e signature 2. / 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 / Ribosomal protein L30e, conserved site / Ribosomal protein L30/YlxQ / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L30e signature 1. / Ribosomal protein L30e signature 2. / 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: 1.8 Å
AuthorsChan, C.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 ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 50S ribosomal protein L30e
B: 50S ribosomal protein L30e
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2518
Polymers21,6752
Non-polymers5766
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-7 kcal/mol
Surface area9590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.245, 64.245, 48.401
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein 50S ribosomal protein L30e / Ribosome


Mass: 10837.556 Da / Num. of mol.: 2 / Mutation: E6A, R92A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus celer (archaea) / Gene: rpl30, rpl30e / Plasmid: pET3C / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: P29160
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.66 Å3/Da / Density % sol: 53.77 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 25% PEG 20000, 0.1M Tris, pH 8.0, 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: Nov 18, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→36.5 Å / Num. obs: 20739 / % possible obs: 100 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 4 / Redundancy: 2.7 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 11.4
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.153 / Mean I/σ(I) obs: 4.9 / % 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: 1.8→32.122 Å / Occupancy max: 1 / Occupancy min: 0.37 / SU ML: 0.26 / σ(F): 2.04 / Phase error: 24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2347 2002 9.67 %RANDOM
Rwork0.1902 ---
all0.1944 20707 --
obs0.1944 20707 99.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.53 Å2 / ksol: 0.366 e/Å3
Displacement parametersBiso max: 65.79 Å2 / Biso mean: 27.5155 Å2 / Biso min: 13.33 Å2
Baniso -1Baniso -2Baniso -3
1-3.0166 Å20 Å2-0 Å2
2--3.0166 Å20 Å2
3----6.0333 Å2
Refinement stepCycle: LAST / Resolution: 1.8→32.122 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1454 0 30 210 1694
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061537
X-RAY DIFFRACTIONf_angle_d1.0142093
X-RAY DIFFRACTIONf_chiral_restr0.059241
X-RAY DIFFRACTIONf_plane_restr0.005265
X-RAY DIFFRACTIONf_dihedral_angle_d11.942572
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8001-1.84510.29181460.228213511497
1.8451-1.8950.29891400.23513261466
1.895-1.95070.2881460.217913271473
1.9507-2.01370.30381440.216813741518
2.0137-2.08570.26891500.202612961446
2.0857-2.16920.24061480.18513461494
2.1692-2.26790.26911240.198313251449
2.2679-2.38740.24261500.200113491499
2.3874-2.53690.28881460.205813391485
2.5369-2.73270.27121320.213251457
2.7327-3.00750.20071520.186613411493
3.0075-3.44230.21261500.167313201470
3.4423-4.33520.17851400.158513411481
4.3352-32.12760.19251340.17213451479

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