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- PDB-3bbd: M. jannaschii Nep1 complexed with S-adenosyl-homocysteine -

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Basic information

Entry
Database: PDB / ID: 3bbd
TitleM. jannaschii Nep1 complexed with S-adenosyl-homocysteine
ComponentsRibosome biogenesis protein NEP1-like
KeywordsTRANSFERASE / methyltransferase / ribosome biogenesis / S-adenosyl-methionine / S-adenosyl-homocysteine / 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
S-ADENOSYL-L-HOMOCYSTEINE / Ribosomal RNA small subunit methyltransferase Nep1
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)50,32111
Polymers48,9082
Non-polymers1,4139
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.894, 91.121, 93.713
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: 24453.844 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-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 3.71 Å3/Da / Density % sol: 66.81 %
Crystal growTemperature: 289 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 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9797 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 18, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 39501 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 30.57 Å2 / Rsym value: 0.107 / Net I/σ(I): 17.5
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 7501 / Rsym value: 0.565 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.15→46.856 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.221 3767 5.02 %random
Rwork0.1798 ---
obs0.1819 39501 99.25 %-
Displacement parametersBiso mean: 37.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.1553 Å20 Å20 Å2
2--2.1253 Å20 Å2
3----2.2806 Å2
Refinement stepCycle: LAST / Resolution: 2.15→46.856 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3372 0 94 265 3731
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.01
X-RAY DIFFRACTIONf_angle_deg1.198
LS refinement shellResolution: 2.15→2.1853 Å
RfactorNum. reflection% reflection
Rfree0.2539 140 -
Rwork0.2158 --
obs-2470 86.73 %

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