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- PDB-5yma: Crystal structure of ribosome assembly factor Efg1 -

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Basic information

Entry
Database: PDB / ID: 5yma
TitleCrystal structure of ribosome assembly factor Efg1
ComponentsPutative rRNA processing protein
KeywordsRIBOSOMAL PROTEIN / 90S pre-ribosome
Function / homologyrRNA-processing protein Efg1 / : / rRNA-processing protein Efg1 / rRNA processing / nucleolus / rRNA-processing protein EFG1
Function and homology information
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.295 Å
AuthorsShu, S. / Ye, K.
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Structural and functional analysis of ribosome assembly factor Efg1.
Authors: Shu, S. / Ye, K.
History
DepositionOct 21, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2018Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 21, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Putative rRNA processing protein


Theoretical massNumber of molelcules
Total (without water)36,3631
Polymers36,3631
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.122, 99.122, 90.179
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Protein Putative rRNA processing protein


Mass: 36362.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0025450 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: G0S5Z3
Has protein modificationY

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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: 3.54 Å3/Da / Density % sol: 65.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2.4M sodium malonate (pH 7.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: Nonius Kappa CCD / Detector: CCD / Date: Dec 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.295→50 Å / Num. obs: 7701 / % possible obs: 99 % / Redundancy: 22 % / Rmerge(I) obs: 0.362 / Net I/σ(I): 19.3
Reflection shellResolution: 3.3→3.36 Å / Redundancy: 20.1 % / Rmerge(I) obs: 1 / Num. unique obs: 385 / CC1/2: 0.952 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.295→38.755 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / Phase error: 23.09
RfactorNum. reflection% reflectionSelection details
Rfree0.2517 730 9.89 %Random selection
Rwork0.1984 ---
obs0.2035 7381 96.01 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 31.37 Å2
Refinement stepCycle: LAST / Resolution: 3.295→38.755 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1493 0 0 0 1493
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2953-3.54960.3511320.27681239X-RAY DIFFRACTION89
3.5496-3.90650.30371440.21671314X-RAY DIFFRACTION96
3.9065-4.4710.22781490.17191351X-RAY DIFFRACTION98
4.471-5.63020.21521470.17581347X-RAY DIFFRACTION98
5.6302-38.7580.19711580.17391400X-RAY DIFFRACTION99

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