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- PDB-1h7m: Ribosomal Protein L30e from Thermococcus celer -

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Basic information

Entry
Database: PDB / ID: 1h7m
TitleRibosomal Protein L30e from Thermococcus celer
Components50S RIBOSOMAL PROTEIN L30ERibosome
KeywordsRIBOSOMAL PROTEIN / RNA-BINDING / RIBOSOME / THERMOPHILIC
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: 1.96 Å
AuthorsChen, Y.W. / Wong, K.B.
Citation
Journal: Biochemistry / Year: 2003
Title: Crystal Structure of Ribosomal Protein L30E from the Extreme Thermophile Thermocccus Celer: Thermal Stability and RNA Binding
Authors: Chen, Y.W. / Bycroft, M. / Wong, K.B.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Crystallization and Preliminary Crystallographic Studies of a Ribosomal Protein L30E from the Hyperthermophilic Archaeon Thermococcus Celer
Authors: Wong, K.B. / Wang, W.K. / Proctor, M.R. / Bycroft, M. / Chen, Y.W.
#2: Journal: J.Mol.Biol. / Year: 1999
Title: Local Folding Coupled to RNA Binding in the Yeast Ribosomal Protein L30
Authors: Mao, H. / Willamson, J.R.
#3: Journal: Nat.Struct.Biol. / Year: 1999
Title: A Novel Loop-Loop Recognition Motif in the Yeast Ribosomal Protein L30 Autoregulatory RNA Complex
Authors: Mao, H. / White, S.A. / Willamson, J.R.
#4: Journal: Science / Year: 2000
Title: The Complete Atomic Structure of the Large Ribosomal Subunit at 2.4 A Resolution
Authors: Ban, N. / Nissen, P. / Hansen, J. / Moore, P.B. / Steitz, T.A.
History
DepositionJul 9, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 4, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4May 1, 2024Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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)10,9951
Polymers10,9951
Non-polymers00
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)48.320, 48.320, 86.420
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein 50S RIBOSOMAL PROTEIN L30E / Ribosome / RPL30E / RPL30


Mass: 10994.643 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOCOCCUS CELER (archaea) / Plasmid: PRSET-A / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P29160
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Compound detailsBELONGS TO THE L30E FAMILY OF RIBOSOMAL PROTEINS.

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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: 2.68 Å3/Da / Density % sol: 54 %
Crystal growpH: 5.6 / Details: 50MM KH2PO4, 20%(W/V) PEG8000, pH 5.60
Crystal grow
*PLUS
Temperature: 290 K / Method: vapor diffusion, hanging drop
Details: Wong, K.B., (2001) Acta Crystallogr.,Sect.D, D57, 865.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
124 mg/mlprotein1drop
250 mMpotassium phosphate1reservoir
320 %(w/v)PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 17, 2000 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.96→24.2 Å / Num. obs: 8226 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 7.6
Reflection shellResolution: 1.96→2.07 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9

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Processing

Software
NameClassification
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: UNPUBLISHED NMR STRUCTURE OF THE SAME L30E PROTEIN

Resolution: 1.96→24.18 Å / SU B: 3.612 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.151
Details: GLY-97 - GLU-100 ARE NOT SEEN IN THE DENISTY MAPS SIDECHAINS OF MET-18, SER-67 AND SER-80 HAVE MULTIPLE CONFORMATIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.225 618 7.5 %RANDOM
Rwork0.165 ---
obs0.17 7608 100 %-
Displacement parametersBiso mean: 21.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.03 Å20.52 Å20 Å2
2--1.03 Å20 Å2
3----1.55 Å2
Refinement stepCycle: LAST / Resolution: 1.96→24.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms729 0 0 120 849
Refinement
*PLUS
Lowest resolution: 24.2 Å / Rfactor obs: 0.17 / Rfactor Rwork: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.028
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.22

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