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- PDB-5dcv: Crystal structure of PhoRpp38-SL12M complex -

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Basic information

Entry
Database: PDB / ID: 5dcv
TitleCrystal structure of PhoRpp38-SL12M complex
Components
  • 50S ribosomal protein L7Ae
  • RNA (47-MER)
KeywordsRNA BINDING PROTEIN/RNA / RNA / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


ribonuclease P activity / tRNA 5'-leader removal / ribosome biogenesis / cytosolic small ribosomal subunit / rRNA binding / structural constituent of ribosome / translation
Similarity search - Function
Ribosomal protein L7Ae, archaea / Ribosomal protein L30/S12 / 60s Ribosomal Protein L30; Chain: A; / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Large ribosomal subunit protein eL8
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
Pyrococcus horikoshii OT3 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.401 Å
AuthorsOshima, K. / Tanaka, Y. / Yao, M.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2016
Title: Structural basis for recognition of a kink-turn motif by an archaeal homologue of human RNase P protein Rpp38
Authors: Oshima, K. / Kakiuchi, Y. / Tanaka, Y. / Ueda, T. / Nakashima, T. / Kimura, M. / Yao, M.
History
DepositionAug 24, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 50S ribosomal protein L7Ae
B: RNA (47-MER)
C: 50S ribosomal protein L7Ae
D: RNA (47-MER)


Theoretical massNumber of molelcules
Total (without water)62,8264
Polymers62,8264
Non-polymers00
Water00
1
A: 50S ribosomal protein L7Ae
B: RNA (47-MER)


Theoretical massNumber of molelcules
Total (without water)31,4132
Polymers31,4132
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-12 kcal/mol
Surface area14010 Å2
MethodPISA
2
C: 50S ribosomal protein L7Ae
D: RNA (47-MER)


Theoretical massNumber of molelcules
Total (without water)31,4132
Polymers31,4132
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-13 kcal/mol
Surface area14040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.090, 79.170, 98.470
Angle α, β, γ (deg.)90.00, 107.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 50S ribosomal protein L7Ae / Ribonuclease P protein component Rpp38 / RNase P component Rpp38 / Ribosomal protein L8e


Mass: 14645.026 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) (archaea)
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
Gene: rpl7ae, PH1496 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P62009
#2: RNA chain RNA (47-MER)


Mass: 16767.936 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Pyrococcus horikoshii OT3 (archaea)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.5 Å3/Da / Density % sol: 64.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 2-prooanol, Mgnessium accetate, sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 11936 / % possible obs: 98.7 % / Redundancy: 3.8 % / Rsym value: 0.047 / Net I/σ(I): 18.85
Reflection shellResolution: 3.4→3.61 Å / Redundancy: 3.8 % / Rmerge(I) obs: 1.162 / Mean I/σ(I) obs: 1.39 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CZW

2czw


Resolution: 3.401→32.398 Å / SU ML: 0.61 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 43.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3113 597 5.01 %
Rwork0.2628 --
obs0.2653 11909 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.401→32.398 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1812 2052 0 0 3864
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064130
X-RAY DIFFRACTIONf_angle_d1.3836062
X-RAY DIFFRACTIONf_dihedral_angle_d21.0211844
X-RAY DIFFRACTIONf_chiral_restr0.059762
X-RAY DIFFRACTIONf_plane_restr0.007414
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4008-3.74260.4211470.38542795X-RAY DIFFRACTION99
3.7426-4.28310.37461490.28642826X-RAY DIFFRACTION99
4.2831-5.39220.30811510.28342827X-RAY DIFFRACTION99
5.3922-32.39970.28321500.23032864X-RAY DIFFRACTION98

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