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- PDB-3dlv: Structures of SRP54 and SRP19, the two proteins assembling the ri... -

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Basic information

Entry
Database: PDB / ID: 3dlv
TitleStructures of SRP54 and SRP19, the two proteins assembling the ribonucleic core of the Signal Recognition Particle from the archaeon Pyrococcus furiosus.
ComponentsSignal recognition particle 19 kDa protein
KeywordsRNA BINDING PROTEIN / PROTEIN-RNA / SIGNAL RECOGNITION PARTICLE / Cytoplasm / Ribonucleoprotein / RNA-binding
Function / homology
Function and homology information


signal recognition particle / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane
Similarity search - Function
Signal recognition particle, SRP19 subunit, archaeal-type / Signal recognition particle, SRP19-like subunit / Signal recognition particle, SRP19 subunit / Signal recognition particle, subunit SRP19-like superfamily / SRP19 protein / Phenylalanyl-tRNA Synthetase; Chain B, domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Signal recognition particle 19 kDa protein
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsEgea, P.F. / Napetschnig, J. / Walter, P. / Stroud, R.M.
CitationJournal: Plos One / Year: 2008
Title: Structures of SRP54 and SRP19, the two proteins that organize the ribonucleic core of the signal recognition particle from Pyrococcus furiosus.
Authors: Egea, P.F. / Napetschnig, J. / Walter, P. / Stroud, R.M.
History
DepositionJun 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 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
Revision 1.3Aug 30, 2023Group: Data collection / Database references / 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
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
B: Signal recognition particle 19 kDa protein
A: Signal recognition particle 19 kDa protein


Theoretical massNumber of molelcules
Total (without water)24,5832
Polymers24,5832
Non-polymers00
Water1,60389
1
B: Signal recognition particle 19 kDa protein


Theoretical massNumber of molelcules
Total (without water)12,2911
Polymers12,2911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Signal recognition particle 19 kDa protein


Theoretical massNumber of molelcules
Total (without water)12,2911
Polymers12,2911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.316, 116.052, 84.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-175-

HOH

21B-182-

HOH

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Components

#1: Protein Signal recognition particle 19 kDa protein / SRP19


Mass: 12291.387 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: DSM3638 / Gene: srp19, PF1894 / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) rosetta2 / References: UniProt: Q8TZT9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 1.76 Å3/Da / Density % sol: 30.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.2-1.3M Na Malonate, 100 mM NaAcetate, 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 / Date: May 8, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.87→50 Å / Num. all: 14745 / Num. obs: 14745 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.9 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 22.3
Reflection shellResolution: 1.87→1.94 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 2 / Num. unique all: 1411 / Rsym value: 0.513 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
ELVESrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DUL

3dul


Resolution: 1.87→47.8 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0.85 / Phase error: 23.59 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1399 10 %10% OF THE NUMBER OF TOTAL REFLECTIONS
Rwork0.199 ---
obs0.205 13987 94.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 65.567 Å2 / ksol: 0.391 e/Å3
Displacement parametersBiso mean: 22 Å2
Baniso -1Baniso -2Baniso -3
1-2.0313 Å20 Å20 Å2
2--1.5372 Å20 Å2
3----3.5685 Å2
Refinement stepCycle: LAST / Resolution: 1.87→47.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1525 0 0 89 1614
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041553
X-RAY DIFFRACTIONf_angle_d0.8122079
X-RAY DIFFRACTIONf_dihedral_angle_d13.765613
X-RAY DIFFRACTIONf_chiral_restr0.054233
X-RAY DIFFRACTIONf_plane_restr0.004263
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.87-1.93790.27571130.21741014101478
1.9379-2.01550.29551330.2027120092
2.0155-2.10720.25811410.18127397
2.7948-3.19910.24241470.2094132498
3.1991-4.03030.26191490.1812133499
4.0303-47.84210.22371560.1903140998

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