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- PDB-7r7o: Structure of methyltransferase domain of Spb1 boudn to SAM -

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Basic information

Entry
Database: PDB / ID: 7r7o
TitleStructure of methyltransferase domain of Spb1 boudn to SAM
ComponentsAdoMet-dependent rRNA methyltransferase SPB1
KeywordsTRANSFERASE / ribosome biogenesis / methyltransferase / nucleolus
Function / homologyS-ADENOSYLMETHIONINE / :
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsCruz, V.E. / Sekulski, K. / Peddada, N. / Erzberger, J.P.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM135617-01 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RR150074 United States
Robert A. Welch FoundationI-1897 United States
CitationJournal: To Be Published
Title: Post-catalytic rRNA binding by the DEAD-box ATPase Spb4 and methyltransferase Spb1 guide the late nucleolar assembly of 60S ribosomes
Authors: Cruz, V.E. / Sekulski, K. / Peddada, N. / Sailer, C. / Balasubramanian, S. / Weirich, C.S. / Stengel, F. / Erzberger, J.P.
History
DepositionJun 25, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AdoMet-dependent rRNA methyltransferase SPB1
B: AdoMet-dependent rRNA methyltransferase SPB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7774
Polymers49,9802
Non-polymers7972
Water9,746541
1
A: AdoMet-dependent rRNA methyltransferase SPB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3892
Polymers24,9901
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: AdoMet-dependent rRNA methyltransferase SPB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3892
Polymers24,9901
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)140.714, 45.497, 92.031
Angle α, β, γ (deg.)90.000, 123.422, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein AdoMet-dependent rRNA methyltransferase SPB1 / 2'-O-ribose RNA methyltransferase / S-adenosyl-L-methionine-dependent methyltransferase


Mass: 24990.193 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SPB1, PACBIOSEQ_LOCUS534 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-pRIL
References: UniProt: A0A7I9D0Y8, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 541 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.46 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20 mM Hepes KOH pH 8 150 mM KCl 0.5 mM TCEP 5% Glycerol 15% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. obs: 66501 / % possible obs: 83.08 % / Redundancy: 8.1 % / Biso Wilson estimate: 14.3 Å2 / CC1/2: 0.982 / CC star: 0.995 / Rpim(I) all: 0.037 / Rrim(I) all: 0.109 / Χ2: 0.89 / Net I/σ(I): 18.1
Reflection shellResolution: 1.58→1.61 Å / Mean I/σ(I) obs: 0.93 / Num. unique obs: 3158 / CC1/2: 0.497 / CC star: 0.815 / Rpim(I) all: 0.037 / Χ2: 0.89

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ELZ

6elz


Resolution: 1.58→42.42 Å / SU ML: 0.1906 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.0965
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2451 1992 3.54 %RANDOM
Rwork0.2291 54282 --
obs0.2297 56274 84.02 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.58→42.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3348 0 54 541 3943
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00683482
X-RAY DIFFRACTIONf_angle_d1.05814716
X-RAY DIFFRACTIONf_chiral_restr0.0642530
X-RAY DIFFRACTIONf_plane_restr0.0053586
X-RAY DIFFRACTIONf_dihedral_angle_d19.9634478
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.620.3156690.25051904X-RAY DIFFRACTION41.53
1.62-1.660.2405860.25262329X-RAY DIFFRACTION51.24
1.66-1.710.2611030.26972802X-RAY DIFFRACTION60.77
1.71-1.770.34881180.28533216X-RAY DIFFRACTION70.49
1.77-1.830.30431340.25273664X-RAY DIFFRACTION79.57
1.83-1.90.28361480.25544023X-RAY DIFFRACTION87.64
1.9-1.990.26991580.24474325X-RAY DIFFRACTION94.26
1.99-2.10.24271650.23724458X-RAY DIFFRACTION96.84
2.1-2.230.25871680.23244583X-RAY DIFFRACTION99.35
2.23-2.40.26461670.2314572X-RAY DIFFRACTION99.31
2.4-2.640.23211660.2334499X-RAY DIFFRACTION97.19
2.64-3.020.23241690.23064610X-RAY DIFFRACTION99.73
3.02-3.810.2371680.21654586X-RAY DIFFRACTION98.14
3.81-42.420.21131730.20424711X-RAY DIFFRACTION98.73

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