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- PDB-3dm9: Structures and Conformations in Solution of the Signal Recognitio... -

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Basic information

Entry
Database: PDB / ID: 3dm9
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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Signal recognition particle receptor FtsY
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 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
DepositionJun 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Signal recognition particle receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1726
Polymers36,6741
Non-polymers4985
Water2,468137
1
B: Signal recognition particle receptor
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)223,03536
Polymers220,0466
Non-polymers2,98830
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation10_666-y+1,-x+1,-z+11
crystal symmetry operation11_656-x+y+1,y,-z+11
crystal symmetry operation12_556x,x-y,-z+11
Buried area17580 Å2
ΔGint-289 kcal/mol
Surface area69300 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)144.600, 144.600, 70.413
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622

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Components

#1: Protein Signal recognition particle receptor / Dpa


Mass: 36674.379 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: DSM3638 / Gene: PF1766 / Plasmid: pET-28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) rosetta2 / References: UniProt: Q8U051
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.9 Å3/Da / Density % sol: 57.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.1-1.5M Ammonium Phosphate, 100 mM Na Acetate, pH 5.0, 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: 0.97949 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 21908 / Num. obs: 21908 / % possible obs: 98.7 % / Observed criterion σ(F): 1 / Redundancy: 13.7 % / Biso Wilson estimate: 39 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 14.9
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 3.9 / Num. unique all: 1738 / Rsym value: 0.63 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
ELVESrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→35.9 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.17 / Phase error: 25.64 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.239 2000 9.18 %9.18% OF RANDOMLY SELECTED REFLECTIONS
Rwork0.203 ---
obs0.206 21777 98.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 65.9 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 40 Å2
Baniso -1Baniso -2Baniso -3
1--9.0822 Å20 Å20 Å2
2---9.0822 Å20 Å2
3---18.1644 Å2
Refinement stepCycle: LAST / Resolution: 2.2→35.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2344 0 20 145 2509
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072397
X-RAY DIFFRACTIONf_angle_d1.0623235
X-RAY DIFFRACTIONf_dihedral_angle_d17.378878
X-RAY DIFFRACTIONf_chiral_restr0.08378
X-RAY DIFFRACTIONf_plane_restr0.004411
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.2-2.26710.29651360.23091354135496
2.2671-2.32840.27091390.2246136597
2.3284-2.39690.30341370.2266136498
3.695-4.2290.1811450.1607143298
4.229-5.32530.19481470.1665145698
5.3253-35.91170.22711520.2366150595

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