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

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Basic information

Entry
Database: PDB / ID: 6fpk
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 / protein homodimerization activity / ATP hydrolysis 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 / protein homodimerization activity / ATP hydrolysis 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: 1.95 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 11, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1653
Polymers6,9291
Non-polymers2362
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint-7 kcal/mol
Surface area5370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.096, 82.555, 29.813
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 6928.821 Da / Num. of mol.: 1 / 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: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.49 Å3/Da / Density % sol: 50.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 21% MPD 0.05M 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: 1.95→46.4 Å / Num. obs: 5318 / % possible obs: 99.66 % / Observed criterion σ(F): 0 / Redundancy: 7.1 % / Rsym value: 0.069 / Net I/σ(I): 19.66
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 3.6 / Num. unique obs: 519 / Rsym value: 0.576 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLMdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QY9

2qy9


Resolution: 1.95→46.4 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.913 / SU B: 3.478 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2338 551 10.4 %RANDOM
Rwork0.21182 ---
obs0.21406 4767 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.575 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å2-0 Å2
2---0.08 Å20 Å2
3---0.27 Å2
Refinement stepCycle: 1 / Resolution: 1.95→46.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms407 0 16 3 426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.019423
X-RAY DIFFRACTIONr_bond_other_d0.0030.02435
X-RAY DIFFRACTIONr_angle_refined_deg2.3532.069570
X-RAY DIFFRACTIONr_angle_other_deg1.253992
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.428552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.626.47117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.7261579
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.218152
X-RAY DIFFRACTIONr_chiral_restr0.120.273
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02445
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0273
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_it3.1152.89211
X-RAY DIFFRACTIONr_mcbond_other3.1112.878210
X-RAY DIFFRACTIONr_mcangle_it3.8224.288262
X-RAY DIFFRACTIONr_mcangle_other3.8184.304263
X-RAY DIFFRACTIONr_scbond_it4.0523.92211
X-RAY DIFFRACTIONr_scbond_other4.0433.977212
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2585.734308
X-RAY DIFFRACTIONr_long_range_B_refined7.94523.766479
X-RAY DIFFRACTIONr_long_range_B_other7.93924.05480
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 41 -
Rwork0.267 361 -
obs--100 %

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