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

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Basic information

Entry
Database: PDB / ID: 3dlu
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 / SRP-dependent cotranslational protein targeting to membrane / 7S RNA binding
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
BROMIDE ION / MALONATE ION / Signal recognition particle 19 kDa protein
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 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 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Signal recognition particle 19 kDa protein
B: Signal recognition particle 19 kDa protein
C: Signal recognition particle 19 kDa protein
D: Signal recognition particle 19 kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,38444
Polymers49,1664
Non-polymers3,21840
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9620 Å2
ΔGint-32 kcal/mol
Surface area17700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.074, 79.699, 60.548
Angle α, β, γ (deg.)90.00, 107.65, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 12291.387 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: DSM3638 / Gene: srp19, PF1894 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) rosetta2 / References: UniProt: Q8TZT9
#2: Chemical...
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 39 / Source method: obtained synthetically / Formula: Br
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.06 Å3/Da / Density % sol: 40.32 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.2-1.3M Na Malonate, 100mM Na Acetate, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.92004 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 3, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92004 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 37519 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.1 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 14.9
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 2.7 / Num. unique all: 3075 / Rsym value: 0.427 / % 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: SAD
Starting model: experimental phasing

Resolution: 1.8→42 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / Phase error: 23.37 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2247 1987 5.46 %5.5% of all reflections
Rwork0.1905 ---
obs0.2247 36384 96.6 %-
all-36384 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.49 Å2 / ksol: 0.382 e/Å3
Displacement parametersBiso mean: 21 Å2
Baniso -1Baniso -2Baniso -3
1--2.0554 Å20 Å2-3.9811 Å2
2---3.5784 Å20 Å2
3---5.6338 Å2
Refinement stepCycle: LAST / Resolution: 1.8→42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2995 0 46 217 3258
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073051
X-RAY DIFFRACTIONf_angle_d1.034091
X-RAY DIFFRACTIONf_dihedral_angle_d13.841214
X-RAY DIFFRACTIONf_chiral_restr0.068458
X-RAY DIFFRACTIONf_plane_restr0.005517
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 (%)
1.8-1.83440.31341220.248214321430.84
1.8344-1.8840.28781300.227823190.92
1.884-1.93940.24991350.214423460.93
2.9903-3.42290.21841420.181925531
3.4229-4.31180.16341510.155125581
4.3118-42.01130.18631600.178125730.99

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