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Basic information

Entry
Database: PDB / ID: 6n6n
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 / 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 / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / Signal recognition particle receptor FtsY
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.877 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 26, 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_atom_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

Downloads & links

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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)67,51711
Polymers66,2022
Non-polymers1,3159
Water8,809489
1
A: Signal recognition particle receptor FtsY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7546
Polymers33,1011
Non-polymers6535
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Signal recognition particle receptor FtsY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7635
Polymers33,1011
Non-polymers6624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.420, 76.883, 106.935
Angle α, β, γ (deg.)90.00, 92.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 498 molecules

#2: Chemical ChemComp-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 489 / 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: 2.21 Å3/Da / Density % sol: 44.43 %
Crystal growTemperature: 297.15 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 0.1 M Bis-Tris, 26% PEG 3350, 215 mM Ammonium acetate, pH 5.8

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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: Jul 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.877→36.171 Å / Num. obs: 46635 / % possible obs: 99.45 % / Redundancy: 2 % / Biso Wilson estimate: 22.3 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.05251 / Rpim(I) all: 0.05251 / Rrim(I) all: 0.07426 / Net I/σ(I): 11.02
Reflection shellResolution: 1.877→1.944 Å

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Processing

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

6cqp


Resolution: 1.877→36.171 Å / SU ML: 0.27 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 28.63
RfactorNum. reflection% reflection
Rfree0.2434 2260 4.85 %
Rwork0.1948 --
obs0.1972 46609 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.877→36.171 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4616 0 79 489 5184
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034810
X-RAY DIFFRACTIONf_angle_d0.556495
X-RAY DIFFRACTIONf_dihedral_angle_d14.7752925
X-RAY DIFFRACTIONf_chiral_restr0.04754
X-RAY DIFFRACTIONf_plane_restr0.003831
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8772-1.91810.39151390.35092598X-RAY DIFFRACTION95
1.9181-1.96270.34511390.31662798X-RAY DIFFRACTION100
1.9627-2.01170.32991350.28212748X-RAY DIFFRACTION100
2.0117-2.06610.30741590.25692765X-RAY DIFFRACTION100
2.0661-2.12690.28721560.24842724X-RAY DIFFRACTION99
2.1269-2.19560.2721400.21542799X-RAY DIFFRACTION100
2.1956-2.2740.24071220.21192777X-RAY DIFFRACTION100
2.274-2.36510.27741550.20342795X-RAY DIFFRACTION100
2.3651-2.47270.27661360.19692748X-RAY DIFFRACTION100
2.4727-2.6030.27311370.19672783X-RAY DIFFRACTION100
2.603-2.7660.27891520.19872785X-RAY DIFFRACTION100
2.766-2.97950.2421480.2012787X-RAY DIFFRACTION100
2.9795-3.27920.2236970.19482845X-RAY DIFFRACTION100
3.2792-3.75320.22471260.16022779X-RAY DIFFRACTION100
3.7532-4.7270.18861600.13982798X-RAY DIFFRACTION100
4.727-36.17770.19391590.17192820X-RAY DIFFRACTION99

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