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- PDB-5l3w: Structure of the crenarchaeal FtsY GTPase bound to GDP -

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Basic information

Entry
Database: PDB / ID: 5l3w
TitleStructure of the crenarchaeal FtsY GTPase bound to GDP
ComponentsSignal recognition particle receptor FtsY
KeywordsPROTEIN TRANSPORT / co-translational protein targeting / Signal Recognition Particle / GTPase
Function / homology
Function and homology information


: / SRP-dependent cotranslational protein targeting to membrane / GTPase activity / GTP binding / plasma membrane / 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
GUANOSINE-5'-DIPHOSPHATE / Signal recognition particle receptor FtsY / Signal recognition particle receptor FtsY
Similarity search - Component
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBange, G. / Wild, K. / Sinning, I.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Structural Basis for Conserved Regulation and Adaptation of the Signal Recognition Particle Targeting Complex.
Authors: Wild, K. / Bange, G. / Motiejunas, D. / Kribelbauer, J. / Hendricks, A. / Segnitz, B. / Wade, R.C. / Sinning, I.
History
DepositionMay 24, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Jan 10, 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)35,1673
Polymers34,6281
Non-polymers5392
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-17 kcal/mol
Surface area15360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.906, 144.906, 49.723
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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


Mass: 34627.551 Da / Num. of mol.: 1 / Fragment: NG domain, UNP residues 69-368
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic)
Gene: ftsY, ATY89_10730, ATZ20_02285 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0U3FSX5, UniProt: P27414*PLUS
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.9 Å3/Da / Density % sol: 57.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M CHES pH 9.0, 10 % (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 25, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.4→41.83 Å / Num. obs: 15249 / % possible obs: 100 % / Redundancy: 5.7 % / Rsym value: 0.088 / Net I/σ(I): 14.9
Reflection shellResolution: 2.4→2.49 Å / Rsym value: 0.536

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L3S chain B

5l3s


Resolution: 2.4→41.831 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 2.03 / Phase error: 22.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2175 1546 10.14 %
Rwork0.1707 --
obs0.1755 15249 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→41.831 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2361 0 33 40 2434
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082428
X-RAY DIFFRACTIONf_angle_d0.9073279
X-RAY DIFFRACTIONf_dihedral_angle_d14.271485
X-RAY DIFFRACTIONf_chiral_restr0.057380
X-RAY DIFFRACTIONf_plane_restr0.005414
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.47760.26831370.20591282X-RAY DIFFRACTION100
2.4776-2.56610.25331500.19531226X-RAY DIFFRACTION100
2.5661-2.66890.26441440.19271245X-RAY DIFFRACTION100
2.6689-2.79030.24531280.1851252X-RAY DIFFRACTION100
2.7903-2.93740.22121510.18831242X-RAY DIFFRACTION100
2.9374-3.12140.24811240.18941256X-RAY DIFFRACTION100
3.1214-3.36230.24831380.20071238X-RAY DIFFRACTION100
3.3623-3.70050.19551400.17291235X-RAY DIFFRACTION100
3.7005-4.23550.21241360.15851260X-RAY DIFFRACTION100
4.2355-5.33450.1921620.15011229X-RAY DIFFRACTION100
5.3345-41.83710.21181360.16171238X-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)
13.40442.3746-0.85421.7182-0.97542.1868-0.04460.2904-0.15080.0650.0377-0.1038-0.10370.1352-0.02150.4328-0.04240.06830.3088-0.06840.3432117.6378113.96092.9179
25.47151.35863.17851.27141.25314.0056-0.2424-0.31950.4641-0.0705-0.07640.3661-0.2431-0.61110.24840.3781-0.0240.05560.4178-0.07140.420283.7452100.0441-0.8324
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 72 through 155 )
2X-RAY DIFFRACTION2chain 'A' and (resid 156 through 368 )

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