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- PDB-1ra4: Crystal structure of the Methanococcus jannaschii L7Ae protein -

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Basic information

Entry
Database: PDB / ID: 1ra4
TitleCrystal structure of the Methanococcus jannaschii L7Ae protein
Components50S ribosomal protein L7Ae
KeywordsSTRUCTURAL PROTEIN / alpha-beta-alpha sandwich fold
Function / homology
Function and homology information


box C/D sno(s)RNA binding / box C/D methylation guide snoRNP complex / ribonuclease P activity / tRNA 5'-leader removal / box C/D snoRNP assembly / ribosome biogenesis / rRNA binding / structural constituent of ribosome / ribosome / translation / 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
Large ribosomal subunit protein eL8
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsSuryadi, J. / Tran, E.J. / Maxwell, E.S. / Brown, B.A.
Citation
Journal: Biochemistry / Year: 2005
Title: The crystal structure of the Methanocaldococcus jannaschii multifunctional L7Ae RNA-binding protein reveals an induced-fit interaction with the box C/D RNAs.
Authors: Suryadi, J. / Tran, E.J. / Maxwell, E.S. / Brown, B.A.
#1: Journal: Embo J. / Year: 2003
Title: Efficient RNA 2'-O-methylation requires juxaposed and symmetrically assembled archaeal box C/D and C'/D' RNPs
Authors: Tran, E.J. / Zhang, X. / Maxwell, E.S.
#2: Journal: Nucleic Acids Res. / Year: 2002
Title: Archaeal ribosomal protein L7 is a functional homolog of the eukaryotic 15.5kD/Snu13p snoRNP core protein
Authors: Kuhn, J.F. / Tran, E.J. / Maxwell, E.S.
History
DepositionOct 31, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 50S ribosomal protein L7Ae


Theoretical massNumber of molelcules
Total (without water)12,9861
Polymers12,9861
Non-polymers00
Water3,801211
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.897, 46.360, 53.975
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 L7Ae


Mass: 12986.119 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: RPL7AE, MJ1203 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS (Novagen) / References: UniProt: P54066
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.11 Å3/Da / Density % sol: 41.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20 % PEG 4000, 10 % isopropanol, 100 mM HEPES-NaOH, pH 7.5 , VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 5, 2002 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.86→35.17 Å / Num. obs: 9674 / % possible obs: 96.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Biso Wilson estimate: 22.7 Å2 / Rsym value: 0.059 / Net I/σ(I): 26.5
Reflection shellResolution: 1.86→1.98 Å / Mean I/σ(I) obs: 12.97 / Num. unique all: 1434 / Rsym value: 0.151 / % possible all: 96.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Threaded model created in SWISS PROT using a composite of the following PDB Entries: 1E7K 1CK2 1JJ2 MOL_ID 8; CHAIN: F

1e7k

1ck2

1jj2


Resolution: 1.86→35.17 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 486425.75 / Data cutoff high rms absF: 486425.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.223 991 10.3 %RANDOM
Rwork0.173 ---
all-9576 --
obs-9576 98.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.7497 Å2 / ksol: 0.41016 e/Å3
Displacement parametersBiso mean: 22.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20 Å20 Å2
2--0.75 Å20 Å2
3----1.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.03 Å
Refinement stepCycle: LAST / Resolution: 1.86→35.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms892 0 0 211 1103
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d1.79
X-RAY DIFFRACTIONr_bond_refined_d0.017
X-RAY DIFFRACTIONr_angle_refined_deg1.531
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.266
X-RAY DIFFRACTIONr_chiral_restr0.138
X-RAY DIFFRACTIONr_gen_planes_refined0.006
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
1.86-1.980.25913790.18513850.022152296.6
1.98-2.130.2531840.1581569
2.13-2.340.2191660.1681572
2.34-2.680.2331760.171600
2.68-3.380.2391840.1721626
3.38-1000.231670.2041687
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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