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- PDB-3e70: Structures and conformations in solution of the Signal Recognitio... -

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Basic information

Entry
Database: PDB / ID: 3.0E+70
TitleStructures and conformations in solution of the Signal Recognition Particle Receptor from the Archaeon Pyrococcus Furiosus
ComponentsSignal recognition particle receptor
KeywordsTRANSPORT PROTEIN / SIGNAL RECOGNITION PARTICLE RECEPTOR / FTSY / SRP-GTPASE / PROTEIN-TARGETING
Function / homology
Function and homology information


signal recognition particle binding / signal-recognition-particle GTPase / SRP-dependent cotranslational protein targeting to membrane / GTPase activity / GTP binding / ATP hydrolysis activity / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
SRP54, nucleotide-binding domain / Signal-recognition particle receptor FtsY / SRP/SRP receptor, N-terminal / 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, nucleotide-binding domain / Signal-recognition particle receptor FtsY / SRP/SRP receptor, N-terminal / 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 / 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
GUANOSINE-5'-DIPHOSPHATE / Signal recognition particle receptor FtsY
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsEgea, P.F. / Tsuruta, H. / Napetschnig, J. / Walter, P. / Stroud, R.M.
CitationJournal: Plos One / Year: 2008
Title: Structures of the signal recognition particle receptor from the archaeon Pyrococcus furiosus: implications for the targeting step at the membrane.
Authors: Egea, P.F. / Tsuruta, H. / de Leon, G.P. / Napetschnig, J. / Walter, P. / Stroud, R.M.
History
DepositionAug 17, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Signal recognition particle receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3514
Polymers36,4401
Non-polymers9113
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)113.122, 53.034, 61.260
Angle α, β, γ (deg.)90.00, 107.42, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Signal recognition particle receptor / Dpa


Mass: 36439.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: DSM3638 / Gene: PF1766 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) ROSETTA2 / References: UniProt: Q8U051
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.41 Å3/Da / Density % sol: 48.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 14-17% PEG 8000 TRIS 100mM pH=8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11588 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 11, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11588 Å / Relative weight: 1
ReflectionResolution: 1.97→58.4 Å / Num. obs: 23541 / % possible obs: 95.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.4 % / Biso Wilson estimate: 41 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 8.7
Reflection shellResolution: 1.97→2.08 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.447 / % possible all: 92.6

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
MOSFLMIN ELVESdata reduction
SCALAIN ELVESdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DMD

3dmd


Resolution: 1.97→29.69 Å
Isotropic thermal model: anistropic TLS refinement applied to the protein
σ(F): 1.34 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflection
Rfree0.263 1999 8.53 %
Rwork0.228 --
obs0.234 23448 95 %
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--11.6098 Å20 Å2-1.9439 Å2
2--22.1336 Å20 Å2
3----10.5238 Å2
Refinement stepCycle: LAST / Resolution: 1.97→29.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2349 0 57 78 2484
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.016
X-RAY DIFFRACTIONf_angle_d1.368
X-RAY DIFFRACTIONf_dihedral_angle_d
X-RAY DIFFRACTIONf_chiral_restr
X-RAY DIFFRACTIONf_plane_restr
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.01390.47581290.39350X-RAY DIFFRACTION1
2.0193-2.07390.39861390.38230X-RAY DIFFRACTION1
2.0739-2.13490.35931440.33130X-RAY DIFFRACTION1
2.1349-2.20380.34451430.28880X-RAY DIFFRACTION1
2.2038-2.28250.32931470.26470X-RAY DIFFRACTION1
4.7421-29.69220.23151350.20860X-RAY DIFFRACTION1

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