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- PDB-2bo1: Crystal structure of a hybrid ribosomal protein L30e with surface... -

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Basic information

Entry
Database: PDB / ID: 2bo1
TitleCrystal structure of a hybrid ribosomal protein L30e with surface residues from T. celer, and core residues from yeast
Components50S RIBOSOMAL PROTEIN L30ERibosome
KeywordsRIBOSOMAL PROTEIN / RIBONUCLEOPROTEIN
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLee, C.F. / Cha, S.S. / Lee, H.S. / Wong, K.B.
CitationJournal: To be Published
Title: Contribution of Hydrophobic Core and Electrostatic Surface to the Thermodyanmic Stability of Ribosomal Protein L30E
Authors: Lee, C.F. / Cha, S.S. / Lee, H.S. / Wong, K.B.
History
DepositionApr 7, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

Downloads & links

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Assembly

Deposited unit
A: 50S RIBOSOMAL PROTEIN L30E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2022
Polymers11,1061
Non-polymers961
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)29.187, 52.531, 52.692
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 50S RIBOSOMAL PROTEIN L30E / Ribosome


Mass: 11105.763 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOCOCCUS CELER (archaea) / Plasmid: PET3D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P29160
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, PHE 4 TO ILE ENGINEERED RESIDUE IN CHAIN A, ALA 11 TO VAL ENGINEERED ...ENGINEERED RESIDUE IN CHAIN A, PHE 4 TO ILE ENGINEERED RESIDUE IN CHAIN A, ALA 11 TO VAL ENGINEERED RESIDUE IN CHAIN A, GLN 12 TO ILE ENGINEERED RESIDUE IN CHAIN A, THR 14 TO SER ENGINEERED RESIDUE IN CHAIN A, ILE 17 TO TYR ENGINEERED RESIDUE IN CHAIN A, VAL 18 TO THR ENGINEERED RESIDUE IN CHAIN A, MET 19 TO LEU ENGINEERED RESIDUE IN CHAIN A, ALA 21 TO TYR ENGINEERED RESIDUE IN CHAIN A, SER 24 TO THR ENGINEERED RESIDUE IN CHAIN A, ILE 25 TO VAL ENGINEERED RESIDUE IN CHAIN A, TYR 27 TO SER ENGINEERED RESIDUE IN CHAIN A, ALA 28 TO LEU ENGINEERED RESIDUE IN CHAIN A, ALA 33 TO SER ENGINEERED RESIDUE IN CHAIN A, VAL 38 TO ILE ENGINEERED RESIDUE IN CHAIN A, ALA 42 TO THR ENGINEERED RESIDUE IN CHAIN A, ILE 46 TO ARG ENGINEERED RESIDUE IN CHAIN A, ILE 50 TO LEU ENGINEERED RESIDUE IN CHAIN A, ILE 59 TO THR ENGINEERED RESIDUE IN CHAIN A, SER 68 TO ASN ENGINEERED RESIDUE IN CHAIN A, LEU 74 TO ALA ENGINEERED RESIDUE IN CHAIN A, LEU 75 TO VAL ENGINEERED RESIDUE IN CHAIN A, ARG 77 TO LYS ENGINEERED RESIDUE IN CHAIN A, ALA 83 TO VAL ENGINEERED RESIDUE IN CHAIN A, LEU 84 TO VAL ENGINEERED RESIDUE IN CHAIN A, ALA 85 TO SER ENGINEERED RESIDUE IN CHAIN A, VAL 86 TO ILE ENGINEERED RESIDUE IN CHAIN A, VAL 87 TO LEU ENGINEERED RESIDUE IN CHAIN A, PRO 89 TO ALA
Sequence detailsTHE AUTHORS SAYS THE ENTRY CAN BE CONSIDERED AS A MUTANT OF T. CELER L30E WITH THE FOLLOWING MUTATIONS

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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: 1.58 Å3/Da / Density % sol: 21.46 %
Crystal growpH: 8.5
Details: 2UL 10MG/ML PROTEIN AND 2UL 22.5% PEG3350, 0.1M TRIS PH 8.5, CRYOPROTECTED IN 20% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 1.12714
DetectorType: BRUKER / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12714 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 9277 / % possible obs: 98.6 % / Observed criterion σ(I): 63 / Redundancy: 5.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 63
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 34 / % possible all: 94.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
HKL-2000data reduction
DENZOdata reduction
HKL-2000data scaling
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H7M

1h7m


Resolution: 1.7→37.19 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.85 / SU B: 1.954 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24 445 4.8 %RANDOM
Rwork0.173 ---
obs0.176 8796 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2---0.14 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.7→37.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms780 0 5 129 914
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022794
X-RAY DIFFRACTIONr_bond_other_d0.0010.02759
X-RAY DIFFRACTIONr_angle_refined_deg1.3051.9931069
X-RAY DIFFRACTIONr_angle_other_deg0.77631761
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5185100
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.28422.90331
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.9115149
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.663157
X-RAY DIFFRACTIONr_chiral_restr0.0780.2124
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02866
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02157
X-RAY DIFFRACTIONr_nbd_refined0.2080.2163
X-RAY DIFFRACTIONr_nbd_other0.1630.2750
X-RAY DIFFRACTIONr_nbtor_refined0.1750.2410
X-RAY DIFFRACTIONr_nbtor_other0.0810.2486
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.267
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.120.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2550.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0970.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.211.5649
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.2082800
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.313339
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4654.5269
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.75 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.234 46
Rwork0.154 588

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