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- PDB-5y7m: Crystal structure of PhoRpp38 bound to a K-turn in P12.1 helix -

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Basic information

Entry
Database: PDB / ID: 5y7m
TitleCrystal structure of PhoRpp38 bound to a K-turn in P12.1 helix
Components
  • 50S ribosomal protein L7Ae
  • RNA (52-MER)
KeywordsRNA BINDING PROTEIN / Kink-turn RNA / Ribonuclease P
Function / homology
Function and homology information


ribonuclease P activity / tRNA 5'-leader removal / ribosome biogenesis / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / cytoplasm
Similarity search - Function
Ribosomal protein L30/S12 / Ribosomal protein L7Ae, archaea / 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 ...Ribosomal protein L30/S12 / Ribosomal protein L7Ae, archaea / 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
GUANOSINE-5'-TRIPHOSPHATE / 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 / molecular replacement / Resolution: 3.1 Å
AuthorsOshima, K. / Kimura, M.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: Crystal structures of the archaeal RNase P protein Rpp38 in complex with RNA fragments containing a K-turn motif.
Authors: Oshima, K. / Gao, X. / Hayashi, S. / Ueda, T. / Nakashima, T. / Kimura, M.
History
DepositionAug 1, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.2Nov 22, 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
Revision 1.3Mar 20, 2024Group: Source and taxonomy / Category: pdbx_entity_src_syn

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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 (52-MER)
C: 50S ribosomal protein L7Ae
D: RNA (52-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,30715
Polymers62,3964
Non-polymers1,91111
Water00
1
A: 50S ribosomal protein L7Ae
B: RNA (52-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0096
Polymers31,1982
Non-polymers8114
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-51 kcal/mol
Surface area15050 Å2
MethodPISA
2
C: 50S ribosomal protein L7Ae
D: RNA (52-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2989
Polymers31,1982
Non-polymers1,1007
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-56 kcal/mol
Surface area15230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.370, 176.600, 59.900
Angle α, β, γ (deg.)90.000, 105.120, 90.000
Int Tables number5
Space group name H-MC121

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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 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P62009
#2: RNA chain RNA (52-MER)


Mass: 16552.934 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Pyrococcus horikoshii OT3 (archaea)
#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4

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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: 4.56 Å3/Da / Density % sol: 73.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: sodium cacodylate ammonium solfate magnesium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→48.376 Å / Num. obs: 20596 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.801 % / Biso Wilson estimate: 57.25 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.197 / Rrim(I) all: 0.229 / Χ2: 0.939 / Net I/σ(I): 7.05 / Num. measured all: 78285
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.1-3.293.8190.7441.9612613332033030.9280.86799.5
3.29-3.513.8130.4623.1211889312931180.9560.53999.6
3.51-3.793.8010.3184.3410959288828830.9720.37199.8
3.79-4.153.8090.2316.0510148267026640.9720.26999.8
4.15-4.643.8420.1668.19356244324350.9770.19399.7
4.64-5.353.8180.1488.928160214121370.9770.17399.8
5.35-6.533.7910.12410.376896181818190.9820.145100
6.53-9.153.750.0715.85314142314170.9940.08299.6
9.15-48.3763.5980.04124.8929508358200.9980.04898.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2czw

2czw


Resolution: 3.1→48.376 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2472 1021 5 %
Rwork0.2249 19415 -
obs0.2261 20436 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 223.77 Å2 / Biso mean: 72.6709 Å2 / Biso min: 36.69 Å2
Refinement stepCycle: final / Resolution: 3.1→48.376 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1928 2264 45 0 4237
Biso mean--127.21 --
Num. residues----354
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0014528
X-RAY DIFFRACTIONf_angle_d0.4656652
X-RAY DIFFRACTIONf_chiral_restr0.031828
X-RAY DIFFRACTIONf_plane_restr0.004444
X-RAY DIFFRACTIONf_dihedral_angle_d17.4492492
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0997-3.26310.44291420.37042711285398
3.2631-3.46750.33581430.31642737288097
3.4675-3.73520.30671460.2872774292099
3.7352-4.11090.2341450.233427582903100
4.1109-4.70530.23831480.195628022950100
4.7053-5.92650.19621480.183928152963100
5.9265-48.38170.18811490.170828182967100

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