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- PDB-5niy: Signal recognition particle-docking protein FtsY -

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Basic information

Entry
Database: PDB / ID: 5niy
TitleSignal recognition particle-docking protein FtsY
ComponentsSignal recognition particle-docking protein FtsY
KeywordsSIGNALING PROTEIN / SRP / GTPase / nucleotide / receptor
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 ...: / 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 / cytoplasm
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
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Signal recognition particle receptor FtsY / Signal recognition particle receptor FtsY
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKempf, G. / Stjepanovic, G. / Lapouge, K. / Sinning, I.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research FoundationSFB TRR83 Germany
German Research FoundationLeibniz Programm Germany
German Research FoundationBZH/Cluster of Excellence:CellNetworks Germany
CitationJournal: Structure / Year: 2018
Title: The Escherichia coli SRP Receptor Forms a Homodimer at the Membrane.
Authors: Kempf, G. / Stjepanovic, G. / Sloan, J. / Hendricks, A. / Lapouge, K. / Sinning, I.
History
DepositionMar 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity.formula_weight
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-docking protein FtsY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5262
Polymers34,0041
Non-polymers5221
Water5,152286
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint-2 kcal/mol
Surface area13600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.730, 80.640, 59.307
Angle α, β, γ (deg.)90.00, 95.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Signal recognition particle-docking protein FtsY


Mass: 34004.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: BK350_09725, BK355_12030, BK400_00245 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1M2U897, UniProt: P10121*PLUS
#2: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.29 Å3/Da / Density % sol: 46.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Ammonium acetate, 0.1 M BIS-TRIS pH 5.5, 17% w/v Polyethylene glycol 10,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976251 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976251 Å / Relative weight: 1
ReflectionResolution: 1.7→47.7 Å / Num. obs: 33675 / % possible obs: 99.8 % / Redundancy: 5.7 % / Net I/σ(I): 14.2
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 3 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YHS

2yhs


Resolution: 1.7→47.648 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.99
RfactorNum. reflection% reflection
Rfree0.1947 1683 5 %
Rwork0.1665 --
obs0.168 33646 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→47.648 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2302 0 32 286 2620
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062398
X-RAY DIFFRACTIONf_angle_d0.8133243
X-RAY DIFFRACTIONf_dihedral_angle_d16.2521472
X-RAY DIFFRACTIONf_chiral_restr0.051378
X-RAY DIFFRACTIONf_plane_restr0.004416
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.75010.27991340.2272646X-RAY DIFFRACTION100
1.7501-1.80650.25971400.20872669X-RAY DIFFRACTION100
1.8065-1.87110.21821380.19442615X-RAY DIFFRACTION100
1.8711-1.9460.24961360.19472668X-RAY DIFFRACTION100
1.946-2.03460.24041510.18842673X-RAY DIFFRACTION100
2.0346-2.14190.2381320.18242639X-RAY DIFFRACTION100
2.1419-2.27610.22151580.17692634X-RAY DIFFRACTION100
2.2761-2.45180.21111510.17552648X-RAY DIFFRACTION100
2.4518-2.69850.19051390.17212685X-RAY DIFFRACTION100
2.6985-3.08890.21061210.17222688X-RAY DIFFRACTION100
3.0889-3.89140.18831310.15052680X-RAY DIFFRACTION100
3.8914-47.66640.13871520.14282718X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.54681.2095-0.20956.7384-0.48394.0258-0.0930.12530.3313-0.40150.1930.88950.1333-0.7226-0.06130.1951-0.0748-0.03820.39370.08770.2687-10.2909-27.978420.6356
25.10650.68510.93082.6691-4.3277.974-0.0398-0.0318-0.1416-0.2452-0.02160.00340.4373-0.37670.06380.2783-0.03390.01130.1706-0.04840.1545-3.7053-34.122411.5334
36.3238-0.29891.00147.6735-4.94187.2176-0.0705-0.3321-0.5164-0.2013-0.0249-0.65070.75780.43970.13050.27410.04550.03170.2129-0.05150.25474.7438-37.299319.4052
40.19110.7879-0.42013.1668-0.55320.5317-0.0238-0.0191-0.02280.00210.07280.02660.0811-0.1175-0.06950.12440.0029-0.00970.19070.00670.15053.635-9.410520.362
51.4719-0.3572-1.00522.2372-0.28013.92760.17450.25840.1054-0.19090.09190.4058-0.2206-0.6616-0.14640.14290.03650.00980.24650.05750.2438-0.07789.735610.0404
64.7240.16420.74562.8985-1.01823.8624-0.03490.40460.2333-0.34830.0313-0.0543-0.0927-0.0720.00760.1724-0.00420.02730.14210.0250.14668.45299.57778.9504
73.19471.96751.02823.4759-0.83672.5353-0.0990.4363-0.1962-0.7210.2425-0.15440.4660.2006-0.10840.27290.01990.0090.2108-0.02780.16989.1253-6.12848.1106
81.42370.0111-0.21084.7624-0.58991.6186-0.0515-0.07830.0648-0.0160.22190.37350.1799-0.2852-0.15190.1367-0.0131-0.03210.16610.03280.154-1.3796-14.841420.8605
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 197 through 224 )
2X-RAY DIFFRACTION2chain 'A' and (resid 225 through 241 )
3X-RAY DIFFRACTION3chain 'A' and (resid 242 through 263 )
4X-RAY DIFFRACTION4chain 'A' and (resid 264 through 320 )
5X-RAY DIFFRACTION5chain 'A' and (resid 321 through 346 )
6X-RAY DIFFRACTION6chain 'A' and (resid 347 through 389 )
7X-RAY DIFFRACTION7chain 'A' and (resid 390 through 453 )
8X-RAY DIFFRACTION8chain 'A' and (resid 454 through 496 )

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