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- PDB-1j8m: Signal Recognition Particle conserved GTPase domain from A. ambivalens -

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Basic information

Entry
Database: PDB / ID: 1j8m
TitleSignal Recognition Particle conserved GTPase domain from A. ambivalens
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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 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 / Resolution: 2 Å
AuthorsMontoya, G. / te Kaat, K. / Moll, R. / Schafer, 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 22, 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 1.3Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)32,8401
Polymers32,8401
Non-polymers00
Water2,864159
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, 72.004
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: 32839.918 Da / Num. of mol.: 1 / Fragment: G-DOMAIN, GTPASE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidianus ambivalens (archaea) / Plasmid: pET-16 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P70722
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 45.94 %
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

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.932
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.932 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 20842
Reflection
*PLUS
Observed criterion σ(I): 0 / Num. measured all: 451808 / Rmerge(I) obs: 0.051

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Processing

Software
NameVersionClassification
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 2→25 Å / SU B: 5.058 / SU ML: 0.145 / SU Rfree: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.196
RfactorNum. reflection% reflectionSelection details
Rfree0.27002 1050 5.1 %random
Rwork0.21639 ---
obs0.21916 19451 99.95 %-
Displacement parametersBiso mean: 22.511 Å2
Baniso -1Baniso -2Baniso -3
1-4.18 Å20 Å20 Å2
2---2.47 Å20 Å2
3----1.71 Å2
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2299 0 0 159 2458
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.022
X-RAY DIFFRACTIONp_angle_deg3.5741.976
X-RAY DIFFRACTIONp_chiral_restr0.1650.2
X-RAY DIFFRACTIONp_xyhbond_nbd0.180.5
X-RAY DIFFRACTIONp_mcbond_it1.1071.5
X-RAY DIFFRACTIONp_mcangle_it1.6152
X-RAY DIFFRACTIONp_scbond_it2.7693
X-RAY DIFFRACTIONp_scangle_it3.964.5
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.29 60
Rwork0.23 1360
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 25 Å / % reflection Rfree: 5.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.011
X-RAY DIFFRACTIONp_angle_deg1.1
X-RAY DIFFRACTIONp_dihedral_angle_d22.4
X-RAY DIFFRACTIONp_improper_angle_d1

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