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- PDB-1ln4: CRYSTAL STRUCTURE OF E. COLI YHBY -

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Basic information

Entry
Database: PDB / ID: 1ln4
TitleCRYSTAL STRUCTURE OF E. COLI YHBY
ComponentsHypothetical protein yhbY
KeywordsRNA BINDING PROTEIN / PUTATIVE RNA-BINDING PROTEIN / PUTATIVE TRANSLATION FACTOR
Function / homology
Function and homology information


rRNA 5'-end processing / preribosome binding / ribosomal small subunit assembly / ribosomal large subunit assembly / RNA binding / cytosol
Similarity search - Function
YhbY-like / RNA-binding, CRM domain / RNA-binding protein YhbY / YhbY-like superfamily / : / CRS1 / YhbY (CRM) domain / CRM domain profile. / CRS1_YhbY / Translation Initiation Factor IF3 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA-binding protein YhbY / RNA-binding protein YhbY
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsOstheimer, G.J. / Barkan, A. / Matthews, B.W.
CitationJournal: Structure / Year: 2002
Title: Crystal structure of E. coli YhbY: a representative of a novel class of RNA binding proteins
Authors: Ostheimer, G.J. / Barkan, A. / Matthews, B.W.
History
DepositionMay 2, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein yhbY


Theoretical massNumber of molelcules
Total (without water)11,7181
Polymers11,7181
Non-polymers00
Water1,928107
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.324, 57.324, 70.895
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Hypothetical protein yhbY / yhbY


Mass: 11717.667 Da / Num. of mol.: 1 / Mutation: N2D,R97L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YHBY / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Gold / References: UniProt: P42550, UniProt: P0AGK4*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.87 Å3/Da / Density % sol: 57.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 200, sodium chloride, tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
150 mM1dropNaCl
210 mMTris1droppH7.0
30.1 mMEDTA1drop
45 mMdithiothreitol1drop
510 mg/mlprotein1drop
645 %(v/v)PEG2001reservoir
7100 mMTris1reservoirpH8.5
8100 mM1reservoirNaCl

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 5.0.210.9611,0.9793,0.9792
SYNCHROTRONALS 5.0.121
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJun 28, 2001
ADSC QUANTUM 42CCDJun 28, 2001
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1DOUBLE CRYSTAL SIMADMx-ray1
2SINGLE CRYSTAL SI CYLINDRICALLY BENTSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.96111
20.97931
30.97921
411
ReflectionResolution: 1.5→20 Å / Num. all: 22101 / Num. obs: 22089 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.6 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 4.5
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.139 / Mean I/σ(I) obs: 4.5 / Num. unique all: 3170 / Rsym value: 0.139 / % possible all: 99.9
Reflection
*PLUS
Num. obs: 22061 / % possible obs: 100 %
Reflection shell
*PLUS
% possible obs: 99.9 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SOLVEphasing
SCALAdata scaling
TNT5Frefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.5→20 Å / Isotropic thermal model: TNT BCORREL V1.0 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: TNT GEOMETRY V1.0
Details: PHASES WERE DETERMINED USING A 3-WAVELENGTH MAD DATASET COLLECTED ON A SINGLE CRYSTAL. THE STRUCTURE WAS REFINED AGAINST AN ADDITIONAL MONOCHROMATIC DATASET THAT WAS COLLECTED USING THE SAME CRYSTAL.
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1119 5 %random
Rwork0.192 ---
all0.193 22103 --
obs0.193 22061 100 %-
Solvent computationBsol: 207.501 Å2 / ksol: 0.82848 e/Å3
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms769 0 0 107 876
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0157770.4
X-RAY DIFFRACTIONt_angle_deg2.76610440.5
X-RAY DIFFRACTIONt_dihedral_angle_d16.1254870
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.004192
X-RAY DIFFRACTIONt_gen_planes0.0111064
X-RAY DIFFRACTIONt_it6.367770.1
X-RAY DIFFRACTIONt_nbd0.0181110
Refinement
*PLUS
Num. reflection obs: 21928 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_angle_deg2.8
X-RAY DIFFRACTIONt_planar_d0.0042
X-RAY DIFFRACTIONt_plane_restr0.0114

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