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- PDB-3a1y: The structure of archaeal ribosomal stalk P1/P0 complex -

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Basic information

Entry
Database: PDB / ID: 3a1y
TitleThe structure of archaeal ribosomal stalk P1/P0 complex
Components
  • 50S ribosomal protein P1 (L12P)
  • Acidic ribosomal protein P0
KeywordsRIBOSOMAL PROTEIN / stalk / helix spin / Ribonucleoprotein
Function / homology
Function and homology information


translational elongation / protein kinase activator activity / ribonucleoprotein complex binding / ribosome biogenesis / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / ribosome / structural constituent of ribosome / translation
Similarity search - Function
Helix Hairpins - #760 / Arc Repressor Mutant, subunit A - #1410 / Ribosomal protein L12, archaea / Ribosomal protein L10, N-terminal RNA-binding domain / Ribosomal protein L12/P1/P2 family / Ribosomal protein P1/P2, N-terminal domain / 50S ribosomal protein L10, archaea / 60s Acidic ribosomal protein / Helix Hairpins / 50S ribosomal protein L10, insertion domain superfamily ...Helix Hairpins - #760 / Arc Repressor Mutant, subunit A - #1410 / Ribosomal protein L12, archaea / Ribosomal protein L10, N-terminal RNA-binding domain / Ribosomal protein L12/P1/P2 family / Ribosomal protein P1/P2, N-terminal domain / 50S ribosomal protein L10, archaea / 60s Acidic ribosomal protein / Helix Hairpins / 50S ribosomal protein L10, insertion domain superfamily / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / Ribosomal protein L10-like domain superfamily / Ribosomal protein L10 / Ribosomal protein L10P / Helix non-globular / Special / Arc Repressor Mutant, subunit A / Alpha-Beta Plaits / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Large ribosomal subunit protein P1 / 50S ribosomal protein L10
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.13 Å
AuthorsNaganuma, T. / Yao, M. / Nomura, N. / Yu, J. / Uchiumi, T. / Tanaka, I.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structural basis for translation factor recruitment to the eukaryotic/archaeal ribosomes
Authors: Naganuma, T. / Nomura, N. / Yao, M. / Mochizuki, M. / Uchiumi, T. / Tanaka, I.
History
DepositionApr 25, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 15, 2014Group: Structure summary
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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 P1 (L12P)
B: 50S ribosomal protein P1 (L12P)
C: 50S ribosomal protein P1 (L12P)
D: 50S ribosomal protein P1 (L12P)
E: 50S ribosomal protein P1 (L12P)
F: 50S ribosomal protein P1 (L12P)
G: Acidic ribosomal protein P0


Theoretical massNumber of molelcules
Total (without water)68,5967
Polymers68,5967
Non-polymers00
Water7,728429
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12730 Å2
ΔGint-135 kcal/mol
Surface area26970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.880, 104.429, 136.223
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 P1 (L12P) / 50S ribosomal protein L12P


Mass: 6240.134 Da / Num. of mol.: 6 / Fragment: N-terminal domain, UNP residues 1-58
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH1998 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O57705
#2: Protein Acidic ribosomal protein P0 / L10E / Acidic ribosomal protein P0 homolog


Mass: 31155.617 Da / Num. of mol.: 1 / Fragment: N-terminal domain, UNP residues 1-284
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH1999 / Plasmid: pET28c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O74109
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 429 / Source method: isolated from a natural source / Formula: H2O

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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: 2.85 Å3/Da / Density % sol: 56.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M MgCl2, 0.1M Na-Acetate trihydrate, 6-10% PEG 6000, pH 4.2-4.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
PH range: 4.2-4.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 11, 2007
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.13→50 Å / Num. all: 44207 / Num. obs: 44207 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 38.8 Å2 / Rmerge(I) obs: 0.106 / Rsym value: 0.106 / Net I/σ(I): 12.4
Reflection shellResolution: 2.13→2.21 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 2 / Num. unique all: 4052 / Rsym value: 0.408 / % possible all: 93

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
SOLVEphasing
RESOLVEphasing
OASISphasing
RefinementMethod to determine structure: SAD / Resolution: 2.13→34.99 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.924 / SU B: 9.806 / SU ML: 0.136 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.223 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26 3131 7.1 %RANDOM
Rwork0.22 ---
all0.223 44207 --
obs0.223 44207 99.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 45.241 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.13→34.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4298 0 0 429 4727
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224344
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5521.9945876
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.185551
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.27326.452186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.97315808
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1481515
X-RAY DIFFRACTIONr_chiral_restr0.1130.2708
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023156
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2360.22332
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.23026
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2281
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.274
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2070.237
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6721.52872
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.10424437
X-RAY DIFFRACTIONr_scbond_it1.81231653
X-RAY DIFFRACTIONr_scangle_it2.8594.51439
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.131→2.186 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 210 -
Rwork0.228 2754 -
obs-2754 91.17 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.48720.6046-1.16455.9935-1.88885.10770.2437-0.28680.29590.3882-0.3502-0.4341-0.43610.23340.1066-0.0902-0.07010.0501-0.1449-0.0675-0.043939.557861.8265109.179
21.3390.40040.54954.17111.15932.92280.12330.01280.09580.1417-0.10950.25990.12920.0135-0.0138-0.13140.01460.0205-0.0660.0125-0.091541.344428.147193.3429
31.4498-0.25550.07931.7281.08443.70410.06660.1371-0.11110.1960.1127-0.05550.45050.2537-0.17930.02080.0769-0.1442-0.09-0.0138-0.091738.56055.419473.1313
41.9925-0.72490.34153.3158-0.24512.74080.10650.1304-0.0851-0.19550.0468-0.33790.29110.2474-0.1533-0.12330.029-0.0157-0.01-0.0671-0.090834.34158.668343.0414
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1G1 - 207
2X-RAY DIFFRACTION2G208 - 233
3X-RAY DIFFRACTION2E1 - 58
4X-RAY DIFFRACTION2F1 - 58
5X-RAY DIFFRACTION3G234 - 259
6X-RAY DIFFRACTION3C1 - 56
7X-RAY DIFFRACTION3D1 - 58
8X-RAY DIFFRACTION4G260 - 283
9X-RAY DIFFRACTION4A1 - 58
10X-RAY DIFFRACTION4B1 - 58

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