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

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Basic information

Entry
Database: PDB / ID: 3dmd
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
Signal-recognition particle receptor FtsY / SRP54, nucleotide-binding domain / 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 ...Signal-recognition particle receptor FtsY / SRP54, nucleotide-binding domain / 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
Signal recognition particle receptor FtsY
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 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: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification
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 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Signal recognition particle receptor
A: Signal recognition particle receptor
C: Signal recognition particle receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,83319
Polymers109,3203
Non-polymers1,51316
Water8,449469
1
B: Signal recognition particle receptor
hetero molecules

B: Signal recognition particle receptor
hetero molecules

A: Signal recognition particle receptor
C: Signal recognition particle receptor
hetero molecules

A: Signal recognition particle receptor
C: Signal recognition particle receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,66638
Polymers218,6396
Non-polymers3,02632
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation3_455x-1/2,y+1/2,z1
crystal symmetry operation4_454-x-1/2,y+1/2,-z-11
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y,-z-11
Buried area14610 Å2
ΔGint-327 kcal/mol
Surface area80250 Å2
MethodPISA
2
B: Signal recognition particle receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8205
Polymers36,4401
Non-polymers3804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Signal recognition particle receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9166
Polymers36,4401
Non-polymers4765
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Signal recognition particle receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0968
Polymers36,4401
Non-polymers6577
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)149.956, 102.368, 101.766
Angle α, β, γ (deg.)90.00, 119.81, 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.: 3
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 469 / 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: 3.1 Å3/Da / Density % sol: 60.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.9-1.2M Lithium Sulfate, 0.4-0.6M Ammonium Sulfate, 100 mM Na Citrate, 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
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 31, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.21→88.4 Å / Num. all: 65992 / Num. obs: 65992 / % possible obs: 98.8 % / Observed criterion σ(F): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 43 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 8.9
Reflection shellResolution: 2.21→2.33 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.766 / Mean I/σ(I) obs: 1.4 / Num. unique all: 9460 / Rsym value: 0.766 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
ELVESrefinement
MOSFLMin ELVESdata reduction
SCALAin ELVESdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DM9

3dm9


Resolution: 2.21→65.06 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.242 2000 3.05 %3.1% OF RANDOMLY SELECTED REFLECTIONS
Rwork0.189 ---
obs0.191 65548 98.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.919 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 42 Å2
Baniso -1Baniso -2Baniso -3
1-2.2675 Å20 Å2-2.9906 Å2
2--0.5839 Å20 Å2
3----3.0836 Å2
Refinement stepCycle: LAST / Resolution: 2.21→65.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7399 0 86 469 7954
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067576
X-RAY DIFFRACTIONf_angle_d0.93910181
X-RAY DIFFRACTIONf_dihedral_angle_d15.8652858
X-RAY DIFFRACTIONf_chiral_restr0.0641174
X-RAY DIFFRACTIONf_plane_restr0.0031295
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 (%)
2.21-2.26530.30781330.274228422892
2.2653-2.32650.30791390.255440996
2.3265-2.3950.30231390.2424442097
3.693-4.22730.17931460.14314650100
4.2273-5.32560.1861480.13574673100
5.3256-65.08560.20751470.1754468099

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