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- PDB-6n9b: FtsY-NG ultra high-resolution -

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Basic information

Entry
Database: PDB / ID: 6n9b
TitleFtsY-NG ultra high-resolution
ComponentsSignal recognition particle receptor FtsY
KeywordsTRANSPORT PROTEIN / FtsY / SRP / Signal recognition particle receptor / SR
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 / SRP54, nucleotide-binding domain / 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 ...Signal-recognition particle receptor FtsY / SRP54, nucleotide-binding domain / 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
ACETATE ION / Signal recognition particle receptor FtsY
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.219 Å
AuthorsAtaide, S.F. / Faoro, C.
CitationJournal: J.Struct.Biol. / Year: 2019
Title: Structural insights into the G-loop dynamics of E. coli FtsY NG domain.
Authors: Faoro, C. / Ataide, S.F.
History
DepositionDec 2, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Mar 18, 2020Group: Database references / Category: citation / Item: _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 2023Group: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,3204
Polymers66,2022
Non-polymers1182
Water14,574809
1
A: Signal recognition particle receptor FtsY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1602
Polymers33,1011
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Signal recognition particle receptor FtsY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1602
Polymers33,1011
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.683, 76.180, 108.786
Angle α, β, γ (deg.)90.00, 93.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 33101.043 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: ftsY, b3464, JW3429
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P10121
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 809 / 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: 2.17 Å3/Da / Density % sol: 43.42 %
Crystal growTemperature: 297.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis-Tris pH 6.6, 24% PEG 2000 MME, 200 mM KBr.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.219→44.2 Å / Num. obs: 165619 / % possible obs: 98.7 % / Redundancy: 2 % / Rmerge(I) obs: 0.029 / Net I/σ(I): 14.75
Reflection shellResolution: 1.219→1.263 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CQP

6cqp


Resolution: 1.219→44.2 Å / SU ML: 0.14 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 18.83
RfactorNum. reflection% reflection
Rfree0.1788 8167 4.93 %
Rwork0.1552 --
obs0.1565 165612 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.219→44.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4633 0 8 809 5450
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124741
X-RAY DIFFRACTIONf_angle_d1.1146386
X-RAY DIFFRACTIONf_dihedral_angle_d16.9421792
X-RAY DIFFRACTIONf_chiral_restr0.08748
X-RAY DIFFRACTIONf_plane_restr0.007831
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2186-1.23250.34722660.31754913X-RAY DIFFRACTION92
1.2325-1.2470.28972700.26365141X-RAY DIFFRACTION97
1.247-1.26220.2982630.25545130X-RAY DIFFRACTION97
1.2622-1.27820.26112690.23465197X-RAY DIFFRACTION97
1.2782-1.2950.25962430.21535167X-RAY DIFFRACTION97
1.295-1.31270.24082720.19765199X-RAY DIFFRACTION98
1.3127-1.33150.21512830.19015224X-RAY DIFFRACTION98
1.3315-1.35130.21892500.17885174X-RAY DIFFRACTION98
1.3513-1.37250.20672650.17565179X-RAY DIFFRACTION98
1.3725-1.3950.22673160.17695226X-RAY DIFFRACTION98
1.395-1.4190.20042610.17025186X-RAY DIFFRACTION98
1.419-1.44480.21362720.17365277X-RAY DIFFRACTION99
1.4448-1.47260.19512760.16385157X-RAY DIFFRACTION98
1.4726-1.50270.19622670.15465265X-RAY DIFFRACTION99
1.5027-1.53530.19372630.13825219X-RAY DIFFRACTION99
1.5353-1.57110.1972480.13575310X-RAY DIFFRACTION99
1.5711-1.61040.17882710.13415254X-RAY DIFFRACTION99
1.6104-1.65390.16112300.13145357X-RAY DIFFRACTION99
1.6539-1.70260.17052560.13575242X-RAY DIFFRACTION99
1.7026-1.75750.15642700.14225304X-RAY DIFFRACTION99
1.7575-1.82030.18762500.14735361X-RAY DIFFRACTION99
1.8203-1.89320.17642850.15415237X-RAY DIFFRACTION100
1.8932-1.97940.183020.14925282X-RAY DIFFRACTION100
1.9794-2.08370.17912900.1495306X-RAY DIFFRACTION100
2.0837-2.21430.16472570.14315346X-RAY DIFFRACTION100
2.2143-2.38530.15962920.14015313X-RAY DIFFRACTION100
2.3853-2.62530.16653150.14945324X-RAY DIFFRACTION100
2.6253-3.00510.19772490.16025376X-RAY DIFFRACTION100
3.0051-3.78580.15933340.15155332X-RAY DIFFRACTION100
3.7858-44.22950.16352820.15355447X-RAY DIFFRACTION100

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