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- PDB-3bbe: M. jannaschii Nep1 -

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Basic information

Entry
Database: PDB / ID: 3bbe
TitleM. jannaschii Nep1
ComponentsRibosome biogenesis protein NEP1-like
KeywordsTRANSFERASE / methyltransferase / ribosome biogenesis / S-adenosyl-methionine / rRNA processing
Function / homology
Function and homology information


rRNA (pseudouridine) methyltransferase activity / rRNA base methylation / Transferases; Transferring one-carbon groups; Methyltransferases / rRNA binding / protein homodimerization activity
Similarity search - Function
Ribosome biogenesis methyltransferase NEP1, archaea / Ribosomal biogenesis, methyltransferase, EMG1/NEP1 / EMG1/NEP1 methyltransferase / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribosomal RNA small subunit methyltransferase Nep1
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsTaylor, A.B. / Meyer, B. / Leal, B.Z. / Kotter, P. / Hart, P.J. / Entian, K.-D. / Wohnert, J.
CitationJournal: Nucleic Acids Res. / Year: 2008
Title: The crystal structure of Nep1 reveals an extended SPOUT-class methyltransferase fold and a pre-organized SAM-binding site.
Authors: Taylor, A.B. / Meyer, B. / Leal, B.Z. / Kotter, P. / Schirf, V. / Demeler, B. / Hart, P.J. / Entian, K.D. / Wohnert, J.
History
DepositionNov 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribosome biogenesis protein NEP1-like
B: Ribosome biogenesis protein NEP1-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,98810
Polymers48,2512
Non-polymers7378
Water4,576254
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.470, 91.088, 94.036
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 Ribosome biogenesis protein NEP1-like /


Mass: 24125.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: Nep1 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q57977
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 3.75 Å3/Da / Density % sol: 67.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 100 mM BisTris-propane, 6-10% polyethylene glycol 400, 30-48% glycerol and 0-400 mM trimethylamine-N-oxide, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.24 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Oct 9, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 37488 / Num. obs: 37488 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 46.43 Å2 / Rsym value: 0.064 / Net I/σ(I): 11.4
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 3700 / Rsym value: 0.49 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 3BBD

3bbd


Resolution: 2.2→41.78 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2461 1869 4.99 %random
Rwork0.2073 ---
obs0.2093 37456 99.87 %-
Displacement parametersBiso mean: 48.79 Å2
Baniso -1Baniso -2Baniso -3
1-0.1079 Å20 Å20 Å2
2--4.7447 Å20 Å2
3----4.8526 Å2
Refinement stepCycle: LAST / Resolution: 2.2→41.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3372 0 48 254 3674
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_deg1.123
LS refinement shellResolution: 2.2→2.2595 Å
RfactorNum. reflection% reflection
Rfree0.3148 129 -
Rwork0.2593 --
obs-2843 99.93 %

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