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- PDB-1jos: Ribosome Binding Factor A(rbfA) -

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Basic information

Entry
Database: PDB / ID: 1jos
TitleRibosome Binding Factor A(rbfA)
ComponentsRIBOSOME-BINDING FACTOR A
KeywordsRNA BINDING PROTEIN / Structure 2 Function Project / S2F / Structural Genomics
Function / homology
Function and homology information


ribosomal small subunit binding / maturation of SSU-rRNA / ribosome biogenesis / cytosol
Similarity search - Function
Ribosome-binding factor A, conserved site / Ribosome-binding factor A signature. / Ribosome-binding factor A / Ribosome-binding factor A domain superfamily / Ribosome-binding factor A / K homology (KH) domain / GMP Synthetase; Chain A, domain 3 / K homology domain-like, alpha/beta / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribosome-binding factor A
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsBonander, N. / Tordova, M. / Howard, A.J. / Eisenstein, E. / Gilliland, G.L. / Structure 2 Function Project (S2F)
CitationJournal: To be Published
Title: The 1.7-A Crystal Structure of HI1288 - Ribosome Binding Factor A (rbfA), a Cold Response Protein
Authors: Bonander, N. / Tordova, M. / Howard, A.J. / Eisenstein, E. / Gilliland, G.L.
History
DepositionJul 30, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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-BINDING FACTOR A


Theoretical massNumber of molelcules
Total (without water)14,8271
Polymers14,8271
Non-polymers00
Water3,045169
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.230, 48.090, 57.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RIBOSOME-BINDING FACTOR A / RBFA


Mass: 14827.134 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: HI1288 / Production host: Escherichia coli (E. coli) / References: UniProt: P45141
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.17 Å3/Da / Density % sol: 43.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 0.6M NaK tartrate, 10 mM HEPES, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 115 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.0113 Å
DetectorType: BRUKER / Detector: CCD / Date: Jun 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0113 Å / Relative weight: 1
ReflectionResolution: 1.7→15 Å / Num. all: 14727 / Num. obs: 10622 / % possible obs: 72 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 12.7
Reflection shellResolution: 1.7→1.74 Å / Mean I/σ(I) obs: 3.5 / Rsym value: 0.32

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SOLVEphasing
CNS1refinement
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.7→15 Å / Rfactor Rfree: 0.283 / Rfactor Rwork: 0.216
Refinement stepCycle: LAST / Resolution: 1.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms817 0 0 169 986
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_d1.6

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