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- PDB-5sum: Ribosome assembly factor NSA1 -

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Basic information

Entry
Database: PDB / ID: 5sum
TitleRibosome assembly factor NSA1
ComponentsRibosome biogenesis protein NSA1
KeywordsRIBOSOMAL PROTEIN / ribosome assembly / rRNA processing / ATPases associated with diverse cellular activities (AAA) / WD40 domain
Function / homologyWDR74/Nsa1 / preribosome, large subunit precursor / ribosomal large subunit biogenesis / rRNA processing / WD40-repeat-containing domain superfamily / nucleolus / nucleus / Ribosome biogenesis protein NSA1
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsLo, Y.H. / Stanley, R.E.
CitationJournal: To Be Published
Title: Ribosome assembly factor
Authors: Lo, Y.H. / Stanley, R.E.
History
DepositionAug 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribosome biogenesis protein NSA1
B: Ribosome biogenesis protein NSA1


Theoretical massNumber of molelcules
Total (without water)104,7722
Polymers104,7722
Non-polymers00
Water37821
1
A: Ribosome biogenesis protein NSA1


Theoretical massNumber of molelcules
Total (without water)52,3861
Polymers52,3861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribosome biogenesis protein NSA1


Theoretical massNumber of molelcules
Total (without water)52,3861
Polymers52,3861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Ribosome biogenesis protein NSA1

B: Ribosome biogenesis protein NSA1


Theoretical massNumber of molelcules
Total (without water)104,7722
Polymers104,7722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_756-y+2,z+1/2,-x+3/21
Buried area2990 Å2
ΔGint-13 kcal/mol
Surface area33140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.086, 163.086, 163.086
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213

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Components

#1: Protein Ribosome biogenesis protein NSA1 / NOP7-associated protein 1


Mass: 52385.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: NSA1, YGL111W, G2990 / Production host: Escherichia coli (E. coli) / References: UniProt: P53136
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 3.45 Å3/Da / Density % sol: 64.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 1.6 M Sodium citrate tribasic / PH range: 6.5-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 35831 / % possible obs: 99.8 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 28.96
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 10 % / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 5.58 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data scaling
PHASERphasing
DMphasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5SUI

5sui


Resolution: 2.8→24.31 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.911 / SU B: 12.084 / SU ML: 0.229 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.517 / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2516 1958 5.7 %RANDOM
Rwork0.2042 ---
obs0.2069 32680 96.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 200 Å2 / Biso mean: 48.085 Å2 / Biso min: 19.93 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.8→24.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6144 0 0 21 6165
Biso mean---30.87 -
Num. residues----782
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0196251
X-RAY DIFFRACTIONr_bond_other_d0.0020.026073
X-RAY DIFFRACTIONr_angle_refined_deg1.8911.9688431
X-RAY DIFFRACTIONr_angle_other_deg1.027313991
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8935772
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.19724.982275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.489151140
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3711527
X-RAY DIFFRACTIONr_chiral_restr0.10.2964
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026945
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021362
X-RAY DIFFRACTIONr_mcbond_it3.8414.6433118
X-RAY DIFFRACTIONr_mcbond_other3.8314.6433117
X-RAY DIFFRACTIONr_mcangle_it5.8466.9383880
LS refinement shellResolution: 2.801→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 145 -
Rwork0.312 2380 -
all-2525 -
obs--97.34 %

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