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- PDB-2yhs: Structure of the E. coli SRP receptor FtsY -

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Basic information

Entry
Database: PDB / ID: 2yhs
TitleStructure of the E. coli SRP receptor FtsY
ComponentsCELL DIVISION PROTEIN FTSY
KeywordsCELL CYCLE / PROTEIN TARGETING / SIMIBI CLASS GTPASE / GTP-BINDING / MEMBRANE / NUCLEOTIDE-BINDING / SIGNAL RECOGNITION PARTICLE / PROTEIN TRANSPORT
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
SRP54, nucleotide-binding 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, nucleotide-binding 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 / 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 speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsStjepanovic, G. / Bange, G. / Wild, K. / Sinning, I.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Lipids Trigger a Conformational Switch that Regulates Signal Recognition Particle (Srp)-Mediated Protein Targeting.
Authors: Stjepanovic, G. / Kapp, K. / Bange, G. / Graf, C. / Parlitz, R. / Wild, K. / Mayer, M.P. / Sinning, I.
History
DepositionMay 5, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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
A: CELL DIVISION PROTEIN FTSY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7086
Polymers55,3981
Non-polymers3105
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.358, 108.412, 31.902
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein CELL DIVISION PROTEIN FTSY / FTSY


Mass: 55397.883 Da / Num. of mol.: 1 / Fragment: NG DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: P10121
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 1.98 Å3/Da / Density % sol: 37.76 % / Description: NONE
Crystal growpH: 7 / Details: 0.1 M HEPES PH 7.0, 30% JEFFAMINE ED-2001 PH 7.0.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 27, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.6→39.7 Å / Num. obs: 38500 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 10.99 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.8
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.7 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FTS

1fts


Resolution: 1.6→39.679 Å / SU ML: 0.19 / σ(F): 0.01 / Phase error: 19.94 / Stereochemistry target values: ML
Details: CRYSTALLIZATION WAS SET UP WITH FULL-LENGTH FTSY. THE MODEL INCLUDES THE NG PLUS 9 STRUCTURE AND THE A DOMAIN IS NOT PRESENT IN THE CRYSTALS.
RfactorNum. reflection% reflection
Rfree0.2198 1824 5 %
Rwork0.1782 --
obs0.1803 36676 98.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.021 Å2 / ksol: 0.386 e/Å3
Displacement parametersBiso mean: 17.55 Å2
Baniso -1Baniso -2Baniso -3
1--0.7037 Å20 Å20 Å2
2--1.4495 Å20 Å2
3----0.7458 Å2
Refinement stepCycle: LAST / Resolution: 1.6→39.679 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 20 214 2603
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062476
X-RAY DIFFRACTIONf_angle_d1.0063335
X-RAY DIFFRACTIONf_dihedral_angle_d15.253948
X-RAY DIFFRACTIONf_chiral_restr0.065386
X-RAY DIFFRACTIONf_plane_restr0.004434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.65720.30971720.27143377X-RAY DIFFRACTION97
1.6572-1.72360.29421600.24433379X-RAY DIFFRACTION97
1.7236-1.8020.25411590.20723372X-RAY DIFFRACTION96
1.802-1.8970.21511890.18053395X-RAY DIFFRACTION97
1.897-2.01590.251520.16553459X-RAY DIFFRACTION98
2.0159-2.17150.21721860.15963492X-RAY DIFFRACTION99
2.1715-2.390.22072020.16113488X-RAY DIFFRACTION100
2.39-2.73580.23552100.17053533X-RAY DIFFRACTION100
2.7358-3.44650.19181840.16663610X-RAY DIFFRACTION100
3.4465-39.69120.18762100.16723747X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -27.5794 Å / Origin y: 12.977 Å / Origin z: -10.8261 Å
111213212223313233
T0.037 Å20.0115 Å2-0.0051 Å2-0.0193 Å2-0.0069 Å2--0.026 Å2
L0.8937 °2-0.1938 °20.2292 °2-0.1795 °2-0.1107 °2--0.2194 °2
S0.0292 Å °0.0694 Å °-0.0818 Å °-0.0216 Å °0.0004 Å °0.0305 Å °0.0133 Å °0.0227 Å °-0.0213 Å °
Refinement TLS groupSelection details: ALL

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