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- PDB-1j8y: Signal Recognition Particle conserved GTPase domain from A. ambiv... -

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Basic information

Entry
Database: PDB / ID: 1j8y
TitleSignal Recognition Particle conserved GTPase domain from A. ambivalens T112A mutant
ComponentsSIGNAL RECOGNITION 54 KDA PROTEIN
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


signal recognition particle / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / GTPase activity / GTP binding / ATP hydrolysis activity
Similarity search - Function
SRP54, nucleotide-binding domain / SRP/SRP receptor, N-terminal / Signal recognition particle, SRP54 subunit / Signal recognition particle, SRP54 subunit, M-domain / Signal recognition particle, SRP54 subunit, M-domain superfamily / Signal peptide binding domain / 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 ...SRP54, nucleotide-binding domain / SRP/SRP receptor, N-terminal / Signal recognition particle, SRP54 subunit / Signal recognition particle, SRP54 subunit, M-domain / Signal recognition particle, SRP54 subunit, M-domain superfamily / Signal peptide binding domain / 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 / Four Helix Bundle (Hemerythrin (Met), subunit A) / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Signal recognition particle 54 kDa protein
Similarity search - Component
Biological speciesAcidianus ambivalens (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2 Å
AuthorsMontoya, G. / te Kaat, K. / Moll, R. / Schaerfer, G. / Sinning, I.
Citation
Journal: Structure Fold.Des. / Year: 2000
Title: The crystal structure of the conserved GTPase of SRP54 from the archaeon Acidianus ambivalens and its comparison with related structures suggests a model for the SRP-SRP receptor complex.
Authors: Montoya, G. / Kaat, K. / Moll, R. / Schafer, G. / Sinning, I.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallization and Preliminary X-ray Diffraction Studies on the Conserved GTPase Domain of the Signal Recognition Particle from Acidianus ambivalens.
Authors: Montoya, G. / te Kaat, K. / Moll, R. / Schafer, G. / Sinning, I.
History
DepositionMay 23, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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 7, 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
F: SIGNAL RECOGNITION 54 KDA PROTEIN


Theoretical massNumber of molelcules
Total (without water)32,8101
Polymers32,8101
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.866, 128.020, 72.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein SIGNAL RECOGNITION 54 KDA PROTEIN / SRP54


Mass: 32809.895 Da / Num. of mol.: 1 / Fragment: G-DOMAIN, GTPASE DOMAIN / Mutation: T112A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidianus ambivalens (archaea) / Plasmid: pET16 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P70722

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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: 2.28 Å3/Da / Density % sol: 46.02 %
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlprotein1drop
2100 mMacetate1reservoir
3100 mMcalcium acetate1reservoir
418 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 21100
Reflection
*PLUS
Lowest resolution: 50 Å / % possible obs: 99.6 % / Num. measured all: 450721 / Rmerge(I) obs: 0.069

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Processing

RefinementMethod to determine structure: MIR / Resolution: 2→500 Å
RfactorNum. reflection% reflection
Rfree0.2586 1043 5.1 %
Rwork0.2267 --
all-20665 -
obs-20502 99.2 %
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--16.267 Å20 Å20 Å2
2--9.486 Å20 Å2
3---6.781 Å2
Refinement stepCycle: LAST / Resolution: 2→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2272 0 0 0 2272
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 500 Å / % reflection Rfree: 5.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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