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- PDB-6n5i: FtsY-NG high-resolution -

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Basic information

Entry
Database: PDB / ID: 6n5i
TitleFtsY-NG 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 / ATP hydrolysis activity / 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 / ATP hydrolysis activity / protein homodimerization 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: 1.498 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
DepositionNov 21, 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 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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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)66,4116
Polymers66,2022
Non-polymers2094
Water14,556808
1
A: Signal recognition particle receptor FtsY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2714
Polymers33,1011
Non-polymers1703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Signal recognition particle receptor FtsY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1402
Polymers33,1011
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.753, 76.207, 108.989
Angle α, β, γ (deg.)90.00, 93.85, 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-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 808 / 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: 2.18 Å3/Da / Density % sol: 43.45 %
Crystal growTemperature: 297.15 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 0.1 M Bis-Tris pH 5.8, 26.5% PEG 2000 MME, 175 mM KBr

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: May 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.498→34.67 Å / Num. obs: 88464 / % possible obs: 97.28 % / Redundancy: 1.8 % / Biso Wilson estimate: 17.54 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.02281 / Rpim(I) all: 0.02281 / Rrim(I) all: 0.03226 / Net I/σ(I): 18.22
Reflection shellResolution: 1.498→1.552 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.1319 / Num. unique all: 8713 / CC1/2: 0.957 / Rpim(I) all: 0.1319 / Rrim(I) all: 0.1865 / % possible all: 96.78

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.498→34.67 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 4.78 / Phase error: 17.55
RfactorNum. reflection% reflection
Rfree0.1818 4326 4.89 %
Rwork0.1329 --
obs0.1352 88458 97.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.498→34.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4633 0 9 808 5450
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034759
X-RAY DIFFRACTIONf_angle_d0.6356410
X-RAY DIFFRACTIONf_dihedral_angle_d18.451807
X-RAY DIFFRACTIONf_chiral_restr0.097749
X-RAY DIFFRACTIONf_plane_restr0.003833
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4985-1.51550.20531330.14372678X-RAY DIFFRACTION93
1.5155-1.53330.23141530.14992792X-RAY DIFFRACTION98
1.5333-1.5520.22751470.14812810X-RAY DIFFRACTION98
1.552-1.57170.21281360.14422848X-RAY DIFFRACTION98
1.5717-1.59240.18481400.1342838X-RAY DIFFRACTION99
1.5924-1.61420.20031460.1382827X-RAY DIFFRACTION99
1.6142-1.63720.18111610.13982833X-RAY DIFFRACTION99
1.6372-1.66170.23811530.13892850X-RAY DIFFRACTION99
1.6617-1.68760.20971460.13682795X-RAY DIFFRACTION99
1.6876-1.71530.17461290.13372874X-RAY DIFFRACTION99
1.7153-1.74490.20621430.13832894X-RAY DIFFRACTION99
1.7449-1.77660.1991480.1392785X-RAY DIFFRACTION99
1.7766-1.81080.17571400.13952859X-RAY DIFFRACTION99
1.8108-1.84770.20811640.13612819X-RAY DIFFRACTION99
1.8477-1.88790.20611240.13742808X-RAY DIFFRACTION98
1.8879-1.93180.18921570.13512873X-RAY DIFFRACTION98
1.9318-1.98010.19161310.12942768X-RAY DIFFRACTION97
1.9801-2.03370.16861510.13252826X-RAY DIFFRACTION98
2.0337-2.09350.18061520.13052778X-RAY DIFFRACTION97
2.0935-2.16110.18391500.12772813X-RAY DIFFRACTION97
2.1611-2.23830.16671310.1212782X-RAY DIFFRACTION97
2.2383-2.32790.18121470.11962813X-RAY DIFFRACTION97
2.3279-2.43390.18411600.12682731X-RAY DIFFRACTION96
2.4339-2.56210.14281110.12792791X-RAY DIFFRACTION95
2.5621-2.72260.19961290.13422803X-RAY DIFFRACTION96
2.7226-2.93280.17691460.13232755X-RAY DIFFRACTION96
2.9328-3.22780.19691570.13432796X-RAY DIFFRACTION96
3.2278-3.69450.15441490.11882751X-RAY DIFFRACTION96
3.6945-4.65340.16031360.1182780X-RAY DIFFRACTION95
4.6534-38.11580.18981560.16762762X-RAY DIFFRACTION93

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