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- PDB-6fpr: Co-translational folding intermediate dictates membrane targeting... -

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Basic information

Entry
Database: PDB / ID: 6fpr
TitleCo-translational folding intermediate dictates membrane targeting of the signal recognition particle (SRP)- receptor
ComponentsSignal recognition particle receptor FtsY
KeywordsMembrane binding protein
Function / homology
Function and homology information


signal recognition particle binding / signal-recognition-particle GTPase / SRP-dependent cotranslational protein targeting to membrane / stringent response / protein targeting / cytoplasmic side of plasma membrane / GTPase activity / GTP binding / ATP hydrolysis activity / protein homodimerization activity ...signal recognition particle binding / signal-recognition-particle GTPase / SRP-dependent cotranslational protein targeting to membrane / stringent response / protein targeting / cytoplasmic side of plasma membrane / GTPase activity / GTP binding / ATP hydrolysis activity / protein homodimerization activity / plasma membrane / cytosol
Similarity search - Function
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 ...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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Signal recognition particle receptor FtsY
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsKarniel, A. / Mrusek, D. / Steinchen, W. / Dym, O. / Bange, G. / Bibi, E.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science FoundationISF 600/11 Israel
CitationJournal: J. Mol. Biol. / Year: 2018
Title: Co-translational Folding Intermediate Dictates Membrane Targeting of the Signal Recognition Particle Receptor.
Authors: Karniel, A. / Mrusek, D. / Steinchen, W. / Dym, O. / Bange, G. / Bibi, E.
History
DepositionFeb 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Signal recognition particle receptor FtsY
B: Signal recognition particle receptor FtsY


Theoretical massNumber of molelcules
Total (without water)13,8582
Polymers13,8582
Non-polymers00
Water905
1
A: Signal recognition particle receptor FtsY


Theoretical massNumber of molelcules
Total (without water)6,9291
Polymers6,9291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Signal recognition particle receptor FtsY


Theoretical massNumber of molelcules
Total (without water)6,9291
Polymers6,9291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)164.573, 35.487, 31.697
Angle α, β, γ (deg.)90.00, 96.48, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Signal recognition particle receptor FtsY / SRP receptor


Mass: 6928.821 Da / Num. of mol.: 2 / Fragment: N Terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: ftsY, b3464, JW3429 / Production host: Escherichia coli (E. coli) / References: UniProt: P10121
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 3.32 Å3/Da / Density % sol: 62.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 22% MPD NaCacodylate pH=6.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.953723 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953723 Å / Relative weight: 1
ReflectionResolution: 2.65→40.88 Å / Num. obs: 5435 / % possible obs: 99.65 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.092 / Rrim(I) all: 0.099 / Net I/σ(I): 15.1
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 781 / Rrim(I) all: 0.586 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QY9

2qy9


Resolution: 2.65→19.93 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.918 / SU B: 10.939 / SU ML: 0.238 / Cross valid method: THROUGHOUT / ESU R: 0.447 / ESU R Free: 0.303 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27699 257 4.7 %RANDOM
Rwork0.23827 ---
obs0.24023 5178 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 52.734 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0.02 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.65→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms849 0 0 5 854
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.019851
X-RAY DIFFRACTIONr_bond_other_d0.0010.02844
X-RAY DIFFRACTIONr_angle_refined_deg1.5972.0141143
X-RAY DIFFRACTIONr_angle_other_deg1.01131951
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7725110
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.49126.57135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.28115170
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.255154
X-RAY DIFFRACTIONr_chiral_restr0.0930.2143
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02928
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02144
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.1145.006446
X-RAY DIFFRACTIONr_mcbond_other4.1055445
X-RAY DIFFRACTIONr_mcangle_it5.9287.47554
X-RAY DIFFRACTIONr_mcangle_other5.9247.476555
X-RAY DIFFRACTIONr_scbond_it5.6355.867405
X-RAY DIFFRACTIONr_scbond_other5.635.868406
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.8778.491590
X-RAY DIFFRACTIONr_long_range_B_refined10.46760.71950
X-RAY DIFFRACTIONr_long_range_B_other10.46660.748951
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.65→2.718 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 16 -
Rwork0.231 363 -
obs--100 %

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