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- PDB-8yeq: Crystal structure of L7/L12 Ribosomal Protein from Mycobacterium ... -

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Basic information

Entry
Database: PDB / ID: 8yeq
TitleCrystal structure of L7/L12 Ribosomal Protein from Mycobacterium tuberculosis
ComponentsLarge ribosomal subunit protein bL12
KeywordsRIBOSOMAL PROTEIN / single crystal / Structural protein / Translational protein
Function / homology
Function and homology information


peptidoglycan-based cell wall / cytosolic large ribosomal subunit / structural constituent of ribosome / translation / mRNA binding / plasma membrane / cytosol
Similarity search - Function
Ribosomal protein L7/L12, oligomerisation / Ribosomal protein L7/L12, oligomerisation domain superfamily / Ribosomal protein L7/L12 dimerisation domain / Ribosomal protein L7/L12 / Ribosomal protein L7/L12, C-terminal / Ribosomal protein L7/L12 C-terminal domain / Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like
Similarity search - Domain/homology
Large ribosomal subunit protein bL12
Similarity search - Component
Biological speciesMycobacterium tuberculosis CDC1551 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsPanicker, L. / Tripathi, P.
Funding support India, 1items
OrganizationGrant numberCountry
Other government India
CitationJournal: Arch.Biochem.Biophys. / Year: 2025
Title: Crystal structure, biophysical characterisation, modeling and docking studies of bL12 ribosomal protein from Mycobacterium tuberculosis.
Authors: Tripathi, P. / Panicker, L.
History
DepositionFeb 23, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Large ribosomal subunit protein bL12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2462
Polymers18,1841
Non-polymers621
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.931, 47.282, 61.637
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Large ribosomal subunit protein bL12 / 50S ribosomal protein L7/L12


Mass: 18183.834 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: His tag, thrombin cleavage site and also extra amino acid from the vector construct are contained.
Source: (gene. exp.) Mycobacterium tuberculosis CDC1551 (bacteria)
Strain: CDC1551 / Gene: rplL / Cell line (production host): pLysS / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P9WHE3
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 1.04 Å3/Da / Density % sol: 12.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M Ammonium Acetate pH 7.0, 25% PEG 8000 25% Ethylene Glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: Excillum MetalJet D2+ 160 kV / Wavelength: 1.36 Å
DetectorType: DECTRIS PILATUS3 R 1M / Detector: PIXEL / Date: Feb 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.36 Å / Relative weight: 1
ReflectionResolution: 1.5→23.9 Å / Num. obs: 12351 / % possible obs: 97.5 % / Redundancy: 9.9 % / CC1/2: 1 / Rmerge(I) obs: 0.024 / Rpim(I) all: 0.008 / Rrim(I) all: 0.026 / Χ2: 1 / Net I/σ(I): 55.1
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 0.093 / Mean I/σ(I) obs: 13.1 / Num. unique obs: 546 / CC1/2: 0.996 / Rpim(I) all: 0.042 / Rrim(I) all: 0.103 / Χ2: 0.67 / % possible all: 85.4

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→23.9 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1943 615 4.99 %
Rwork0.166 --
obs0.1674 12314 97.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→23.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms527 0 4 105 636
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006548
X-RAY DIFFRACTIONf_angle_d0.761736
X-RAY DIFFRACTIONf_dihedral_angle_d5.34578
X-RAY DIFFRACTIONf_chiral_restr0.05291
X-RAY DIFFRACTIONf_plane_restr0.00494
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.650.22281350.16392718X-RAY DIFFRACTION92
1.65-1.890.20311640.16652907X-RAY DIFFRACTION98
1.89-2.380.17821470.16572989X-RAY DIFFRACTION99
2.38-23.90.19511690.16653085X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -0.0932 Å / Origin y: 16.345 Å / Origin z: 11.9134 Å
111213212223313233
T0.0739 Å20.0007 Å2-0.0014 Å2-0.0726 Å2-0.0005 Å2--0.0646 Å2
L1.0336 °2-0.2949 °2-0.095 °2-0.9537 °20.2428 °2--0.4929 °2
S-0.0134 Å °0.0617 Å °0.0351 Å °-0.0394 Å °-0.0141 Å °-0.0168 Å °-0.0141 Å °-0.0226 Å °-0.0018 Å °
Refinement TLS groupSelection details: all

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