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- PDB-5sui: Ribosome assembly factor NSA1: C-terminal truncation -

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Basic information

Entry
Database: PDB / ID: 5sui
TitleRibosome assembly factor NSA1: C-terminal truncation
ComponentsRibosome biogenesis protein NSA1
KeywordsPROTEIN BINDING / 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 / SAD / Resolution: 1.3 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 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribosome biogenesis protein NSA1


Theoretical massNumber of molelcules
Total (without water)49,1791
Polymers49,1791
Non-polymers00
Water7,927440
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.327, 81.052, 87.371
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 49179.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's 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.: 440 / 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: 1.84 Å3/Da / Density % sol: 37.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20.1%(v/v) PEG 1500, 13.4%(v/v) PEG 400, 0.1M HEPES/ Sodium hydroxide pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→59.42 Å / Num. obs: 93271 / % possible obs: 99.9 % / Redundancy: 7.2 % / Net I/σ(I): 29.6

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
SOLVEphasing
RESOLVEphasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.3→59.42 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.467 / SU ML: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.04 / ESU R Free: 0.041
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1618 1994 2.1 %RANDOM
Rwork0.1289 ---
obs0.1296 93271 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 89.21 Å2 / Biso mean: 21.961 Å2 / Biso min: 10.15 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 1.3→59.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3007 0 0 440 3447
Biso mean---32.62 -
Num. residues----382
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0193061
X-RAY DIFFRACTIONr_bond_other_d0.0020.022989
X-RAY DIFFRACTIONr_angle_refined_deg2.4291.9664123
X-RAY DIFFRACTIONr_angle_other_deg1.22536890
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3575378
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.63424.737133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.27715566
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6871514
X-RAY DIFFRACTIONr_chiral_restr0.190.2468
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.023394
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02672
X-RAY DIFFRACTIONr_mcbond_it3.5351.8581524
X-RAY DIFFRACTIONr_mcbond_other3.4811.8571523
X-RAY DIFFRACTIONr_mcangle_it3.8512.7821898
X-RAY DIFFRACTIONr_rigid_bond_restr6.12336050
X-RAY DIFFRACTIONr_sphericity_free24.874593
X-RAY DIFFRACTIONr_sphericity_bonded12.59756343
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 147 -
Rwork0.217 6735 -
all-6882 -
obs--98.89 %

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