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- PDB-2pxb: Variant 2 of Ribonucleoprotein Core of the E. Coli Signal Recogni... -

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Basic information

Entry
Database: PDB / ID: 2pxb
TitleVariant 2 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle
Components
  • 4.5 S RNA
  • Signal recognition particle protein
KeywordsSIGNALING PROTEIN/RNA / GU PAIR / HEXAMINE / RNA PHASING / RNA / CATION BINDING / SIGNALING PROTEIN-RNA COMPLEX
Function / homology
Function and homology information


signal recognition particle / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / protein targeting to membrane / ribonucleoprotein complex / GTPase activity / GTP binding / ATP hydrolysis activity / cytosol
Similarity search - Function
Signal recognition particle, SRP54 subunit, M-domain / Signal recognition particle protein / Signal recognition particle, SRP54 subunit / Signal recognition particle, SRP54 subunit, M-domain / Signal recognition particle, SRP54 subunit, M-domain superfamily / Signal peptide binding domain / SRP54-type proteins GTP-binding domain signature. / Signal recognition particle SRP54, helical bundle / Signal recognition particle SRP54, N-terminal domain superfamily / SRP54-type protein, helical bundle domain ...Signal recognition particle, SRP54 subunit, M-domain / Signal recognition particle protein / Signal recognition particle, SRP54 subunit / Signal recognition particle, SRP54 subunit, M-domain / Signal recognition particle, SRP54 subunit, M-domain superfamily / Signal peptide binding domain / SRP54-type proteins GTP-binding domain signature. / Signal recognition particle SRP54, helical bundle / Signal recognition particle SRP54, N-terminal domain superfamily / SRP54-type protein, helical bundle domain / SRP54-type protein, helical bundle domain / Signal recognition particle, SRP54 subunit, GTPase domain / SRP54-type protein, GTPase domain / SRP54-type protein, GTPase domain / 434 Repressor (Amino-terminal Domain) / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
COBALT HEXAMMINE(III) / RNA / RNA (> 10) / Signal recognition particle protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKeel, A.Y. / Rambo, R.P. / Batey, R.T. / Kieft, J.S.
CitationJournal: Structure / Year: 2007
Title: A General Strategy to Solve the Phase Problem in RNA Crystallography.
Authors: Keel, A.Y. / Rambo, R.P. / Batey, R.T. / Kieft, J.S.
History
DepositionMay 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 10, 2017Group: Refinement description
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Refinement description
Category: database_2 / refine_hist ...database_2 / refine_hist / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 4.5 S RNA
A: Signal recognition particle protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,51110
Polymers28,2222
Non-polymers1,2898
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.981, 78.684, 32.274
Angle α, β, γ (deg.)90.000, 94.860, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: RNA chain 4.5 S RNA


Mass: 15885.515 Da / Num. of mol.: 1 / Fragment: DOMAIN IV / Mutation: C132U, U133G, A175U
Source method: isolated from a genetically manipulated source
#2: Protein Signal recognition particle protein / Fifty-four homolog / p48


Mass: 12336.646 Da / Num. of mol.: 1 / Fragment: C TERMINAL DOMAIN (RESIDUES 328-432)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ffh / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(pLysS) / References: UniProt: P0AGD7
#3: Chemical
ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CoH18N6
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: 2.94 Å3/Da / Density % sol: 58.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 20Mm NaOH-MES pH 5.6, 200mM KCl, 10% Isopropanol, 5mM Cobalt Hexamine, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1NaOH-MES11
2KCl11
3Isopropanol11
4H2O11
5NaOH-MES12
6KCl12
7Isopropanol12

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11131
21
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Feb 18, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→39.34 Å / Num. obs: 10959 / % possible obs: 96.4 % / Redundancy: 7.72 % / Rmerge(I) obs: 0.065 / Χ2: 1.01 / Net I/σ(I): 18.7 / Scaling rejects: 641
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 7.59 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 4.8 / Num. measured all: 8128 / Num. unique all: 1071 / Χ2: 0.72 / % possible all: 96.1

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Phasing

Phasing MRCor.coef. Fo:Fc: 0.86 / Packing: 0.392
Highest resolutionLowest resolutionMethodReflection percentσ(F)
Translation4 Å15 Ågeneral97.6 0

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Processing

Software
NameVersionClassificationNB
d*TREK9.4Ldata scaling
CNSrefinement
PDB_EXTRACT2data extraction
CrystalCleardata collection
d*TREKdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DUL

1dul


Resolution: 2.5→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2722 2046 4.7 %
Rwork0.254 --
obs-21420 49.3 %
Solvent computationBsol: 45 Å2
Displacement parametersBiso mean: 56.38 Å2
Baniso -1Baniso -2Baniso -3
1-11.864 Å20 Å25.842 Å2
2---17.672 Å20 Å2
3---5.807 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms533 1052 56 0 1641
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param
X-RAY DIFFRACTION5CNS_TOPPAR:cohex.param

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