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- PDB-2pxe: Variant 4 of Ribonucleoprotein Core of the E. Coli Signal Recogni... -

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Basic information

Entry
Database: PDB / ID: 2pxe
TitleVariant 4 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 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 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 20, 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)29,3509
Polymers28,2222
Non-polymers1,1287
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.480, 73.410, 33.160
Angle α, β, γ (deg.)90.00, 94.65, 90.00
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: C132G, A175G, G176U / Source method: obtained synthetically / Details: synthetic
#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.: 7 / 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: 2.85 Å3/Da / Density % sol: 56.8 %
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
4Cobalt Hexamine11
5H2O11
6NaOH-MES12
7KCl12
8Isopropanol12
9Cobalt Hexamine12

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jul 21, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→37.75 Å / Num. obs: 40894 / % possible obs: 97.1 % / Redundancy: 3.57 % / Rmerge(I) obs: 0.121 / Χ2: 0.97 / Net I/σ(I): 6.5 / Scaling rejects: 1103
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2-2.073.390.3862.91343939640.9292.7
2.07-2.153.520.3831429140530.9797.2
2.15-2.253.510.3653.2141464016195.8
2.25-2.373.50.3593.31450141311.0696.2
2.37-2.523.50.3273.51437240911.0298.1
2.52-2.713.510.2933.91430540611.0397.7
2.71-2.993.530.2074.91471541430.9997.9
2.99-3.423.610.1097.61496841190.9498.5
3.42-4.313.760.06812.41590641870.8899.1
4.31-37.753.810.05318.41629741290.8697.8

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Phasing

Phasing MRCor.coef. Fo:Fc: 0.72 / Packing: 0.29
Highest resolutionLowest resolutionMethodReflection percentσ(F)
Translation2.15 Å40 Ågeneral97.2 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 1DUL

1dul


Resolution: 2→50 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2768 3993 9.5 %
Rwork0.2338 --
obs-40729 96.7 %
Solvent computationBsol: 49.911 Å2
Displacement parametersBiso mean: 29.895 Å2
Baniso -1Baniso -2Baniso -3
1-1.095 Å20 Å20.467 Å2
2---3.299 Å20 Å2
3---2.204 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms533 1052 49 0 1634
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param
X-RAY DIFFRACTION4CNS_TOPPAR:cohex.param
X-RAY DIFFRACTION5CNS_TOPPAR:water_rep.param

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