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- PDB-9l6z: Crystal structure of the L7Ae derivative protein LS12 in RNA-free... -

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Basic information

Entry
Database: PDB / ID: 9l6z
TitleCrystal structure of the L7Ae derivative protein LS12 in RNA-free state
ComponentsLarge ribosomal subunit protein eL8
KeywordsRNA BINDING PROTEIN / Protein-RNA complex
Function / homology
Function and homology information


ribonuclease P activity / tRNA 5'-leader removal / ribosome biogenesis / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / cytoplasm
Similarity search - Function
Ribosomal protein L7Ae, archaea / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae signature. / Ribosomal protein L7Ae/L8/Nhp2 family / : / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like
Similarity search - Domain/homology
Large ribosomal subunit protein eL8
Similarity search - Component
Biological speciesArchaeoglobus fulgidus DSM 4304 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTeramoto, T. / Nakashima, M. / Fukunaga, K. / Yokobayashi, Y. / Kakuta, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19K15701 Japan
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: Structural insights into lab-coevolved RNA-RBP pairs and applications of synthetic riboswitches in cell-free system.
Authors: Fukunaga, K. / Teramoto, T. / Nakashima, M. / Ohtani, T. / Katsuki, R. / Matsuura, T. / Yokobayashi, Y. / Kakuta, Y.
History
DepositionDec 25, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Large ribosomal subunit protein eL8
B: Large ribosomal subunit protein eL8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3157
Polymers26,2002
Non-polymers1155
Water4,720262
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-44 kcal/mol
Surface area12170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.800, 54.270, 54.866
Angle α, β, γ (deg.)90.00, 93.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Large ribosomal subunit protein eL8 / 50S ribosomal protein L7Ae / Ribosomal protein L8e


Mass: 13100.113 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus DSM 4304 (archaea)
Strain: ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16
Gene: rpl7ae, AF_0764 / Production host: Escherichia coli (E. coli) / References: UniProt: O29494
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.92 Å3/Da / Density % sol: 35.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 30% PEG 2,000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 35224 / % possible obs: 97.5 % / Redundancy: 3.2 % / CC1/2: 0.991 / Rrim(I) all: 0.133 / Net I/σ(I): 15.86
Reflection shellResolution: 1.8→1.91 Å / % possible obs: 86.5 % / Redundancy: 2.2 % / Num. unique obs: 5019 / CC1/2: 0.867 / Rrim(I) all: 0.419

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BW0

4bw0


Resolution: 1.8→38.54 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2135 1756 4.99 %
Rwork0.1711 --
obs0.1732 35222 97.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→38.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1838 0 5 262 2105
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.953
X-RAY DIFFRACTIONf_dihedral_angle_d16.464792
X-RAY DIFFRACTIONf_chiral_restr0.058307
X-RAY DIFFRACTIONf_plane_restr0.007341
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.26741060.23232118X-RAY DIFFRACTION81
1.85-1.90.27511270.21352400X-RAY DIFFRACTION91
1.9-1.960.24811420.19292632X-RAY DIFFRACTION99
1.96-2.030.24871250.16052625X-RAY DIFFRACTION100
2.03-2.110.24941370.17082682X-RAY DIFFRACTION100
2.12-2.210.21231330.16772624X-RAY DIFFRACTION100
2.21-2.330.23451580.17642588X-RAY DIFFRACTION100
2.33-2.470.19621230.1812667X-RAY DIFFRACTION100
2.47-2.660.21291370.18212646X-RAY DIFFRACTION100
2.66-2.930.24641250.18272611X-RAY DIFFRACTION100
2.93-3.360.19981430.17342663X-RAY DIFFRACTION100
3.36-4.230.18561550.13932604X-RAY DIFFRACTION99
4.23-38.540.17221450.15682606X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -8.8471 Å / Origin y: -17.7225 Å / Origin z: 39.9407 Å
111213212223313233
T0.0386 Å2-0.0032 Å20.0032 Å2-0.0913 Å2-0.0134 Å2--0.0681 Å2
L0.3305 °2-0.1034 °20.0557 °2-1.8114 °2-1.0927 °2--1.2743 °2
S-0.0038 Å °-0.0553 Å °0.0133 Å °0.1012 Å °0.0338 Å °0.0294 Å °-0.0157 Å °-0.024 Å °-0.0258 Å °
Refinement TLS groupSelection details: all

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