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- PDB-1rlg: Molecular basis of Box C/D RNA-protein interaction: co-crystal st... -

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Basic information

Entry
Database: PDB / ID: 1rlg
TitleMolecular basis of Box C/D RNA-protein interaction: co-crystal structure of the Archaeal sRNP intiation complex
Components
  • 25-MER
  • 50S ribosomal protein L7AeRibosome
KeywordsStructural Protein/RNA / PROTEIN-RNA / Structural 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 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 speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsMoore, T. / Zhang, Y. / Fenley, M.O. / Li, H.
CitationJournal: STRUCTURE / Year: 2004
Title: Molecular Basis of Box C/D RNA-Protein Interactions; Cocrystal Structure of Archaeal L7Ae and a Box C/D RNA.
Authors: Moore, T. / Zhang, Y. / Fenley, M.O. / Li, H.
History
DepositionNov 25, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 25-MER
D: 25-MER
A: 50S ribosomal protein L7Ae
B: 50S ribosomal protein L7Ae


Theoretical massNumber of molelcules
Total (without water)43,0844
Polymers43,0844
Non-polymers00
Water0
1
C: 25-MER
A: 50S ribosomal protein L7Ae


Theoretical massNumber of molelcules
Total (without water)21,5422
Polymers21,5422
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: 25-MER
B: 50S ribosomal protein L7Ae


Theoretical massNumber of molelcules
Total (without water)21,5422
Polymers21,5422
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.584, 120.584, 120.584
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number195
Space group name H-MP23
DetailsThe biological assembly is packed by a dimmer in the asymmetric unit by the operations of space group P23

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Components

#1: RNA chain 25-MER


Mass: 8329.573 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein 50S ribosomal protein L7Ae / Ribosome


Mass: 13212.320 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: RPL7AE, AF0764 / Plasmid: pET13 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O29494

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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: 3.66 Å3/Da / Density % sol: 66.12 %
Crystal growTemperature: 303 K / Method: evaporation / pH: 7.5
Details: PEG 400,magnesium acetate, HEPES , pH 7.5, EVAPORATION, temperature 303K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 40011
2magnesium acetate11
3HEPES11
4H2O11
5PEG 40012
6magnesium acetate12
7H2O12

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Data collection

DiffractionMean temperature: 263 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.99, 1.09, 0.97
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Apr 16, 2003
RadiationMonochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.991
21.091
30.971
ReflectionResolution: 2.7→29.25 Å / Num. obs: 30750 / % possible obs: 0.94 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 80.7 Å2
Reflection shellResolution: 2.7→2.71 Å / % possible all: 54

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.7→29.25 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 324127.19 / Data cutoff high rms absF: 324127.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.26 2706 9.3 %RANDOM
Rwork0.235 ---
all0.235 30802 --
obs0.235 28953 94 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.1653 Å2 / ksol: 0.290896 e/Å3
Displacement parametersBiso mean: 61.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.54 Å0.51 Å
Refinement stepCycle: LAST / Resolution: 2.7→29.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1774 1078 0 0 2852
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d2.78
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.396 348 8.5 %
Rwork0.379 3738 -
obs--78.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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