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- PDB-3o7b: Crystal structure of Archaeoglobus Fulgidus Nep1 bound to S-adeno... -

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Basic information

Entry
Database: PDB / ID: 3o7b
TitleCrystal structure of Archaeoglobus Fulgidus Nep1 bound to S-adenosylhomocysteine
ComponentsRibosome biogenesis Nep1 RNA methyltransferase
KeywordsTRANSFERASE / SPOUT / ribosome biogenesis / methyltransferase / rRNA processing
Function / homology
Function and homology information


rRNA (pseudouridine) methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / rRNA binding
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 / TYROSINE / Ribosomal RNA small subunit methyltransferase Nep1
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 1.45 Å
AuthorsThomas, S.R. / LaRonde-LeBlanc, N.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: Structural insight into the functional mechanism of Nep1/Emg1 N1-specific pseudouridine methyltransferase in ribosome biogenesis.
Authors: Thomas, S.R. / Keller, C.A. / Szyk, A. / Cannon, J.R. / Laronde-Leblanc, N.A.
History
DepositionJul 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribosome biogenesis Nep1 RNA methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9483
Polymers28,3831
Non-polymers5662
Water4,324240
1
A: Ribosome biogenesis Nep1 RNA methyltransferase
hetero molecules

A: Ribosome biogenesis Nep1 RNA methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8966
Polymers56,7652
Non-polymers1,1314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area2420 Å2
ΔGint-9 kcal/mol
Surface area18830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.083, 70.083, 95.190
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsAfNep1 is a biological dimer by symmetry operation x,y,z.

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Components

#1: Protein Ribosome biogenesis Nep1 RNA methyltransferase


Mass: 28382.510 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: AF_0734 / Plasmid: pdest527 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O29524
#2: Chemical ChemComp-TYR / TYROSINE / Tyrosine


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO3
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.38 Å3/Da / Density % sol: 48.27 %
Crystal growTemperature: 293 K
Details: 3-4M NaCl, 0.1M HEPES, pH 7.0-8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
PH range: 7.0-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.99998
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 15, 2007
RadiationMonochromator: KOHZU HLD8-24 / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 1.45→28.9 Å / Num. obs: 48192 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 14.3 % / Rsym value: 0.075 / Net I/σ(I): 32.9
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 10 % / Mean I/σ(I) obs: 5.8 / Rsym value: 0.517 / % possible all: 100

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Phasing

Phasing
Method
SAD
molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.1data extraction
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.45→28.9 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.958 / Occupancy max: 1 / Occupancy min: 0 / SU B: 1.15 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.211 2437 5.1 %RANDOM
Rwork0.198 ---
obs0.199 48192 99.8 %-
all-48192 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.45 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.45→28.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1753 0 38 240 2031
LS refinement shellResolution: 1.452→1.49 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 173 -
Rwork0.265 3315 -
all-3488 -
obs--98.81 %

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