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- PDB-6cqp: High resolution crystal structure of FtsY-NG domain of E. coli -

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Basic information

Entry
Database: PDB / ID: 6cqp
TitleHigh resolution crystal structure of FtsY-NG domain of E. coli
ComponentsSignal recognition particle receptor FtsY
KeywordsPROTEIN TRANSPORT / cotranslational delivery SRP
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 / 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: 1.446 Å
AuthorsFaoro, C. / Ataide, S.F.
CitationJournal: PLoS ONE / Year: 2018
Title: Discovery of fragments that target key interactions in the signal recognition particle (SRP) as potential leads for a new class of antibiotics.
Authors: Faoro, C. / Wilkinson-White, L. / Kwan, A.H. / Ataide, S.F.
History
DepositionMar 15, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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.ptnr1_symmetry / _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_label_seq_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)66,59313
Polymers66,2022
Non-polymers39111
Water14,268792
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-81 kcal/mol
Surface area25920 Å2
Unit cell
Length a, b, c (Å)34.697, 76.105, 108.871
Angle α, β, γ (deg.)90.00, 93.64, 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 792 / 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: 43.24 %
Crystal growTemperature: 297.15 K / Method: vapor diffusion, sitting drop / pH: 6.2 / Details: 0.1 M Bis-Tris pH 6.2, 28% PEG3350, 165mM NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.953724980354 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: 0.953724980354 Å / Relative weight: 1
ReflectionResolution: 1.4461→38.05 Å / Num. obs: 99964 / % possible obs: 99.2 % / Redundancy: 2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.02088 / Net I/σ(I): 20.69
Reflection shellResolution: 1.4461→1.498 Å / Redundancy: 2.73 % / Rmerge(I) obs: 0.08924 / Num. unique all: 9458 / CC1/2: 0.979

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FTS

1fts


Resolution: 1.446→44.216 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1772 4812 4.81 %
Rwork0.132 --
obs0.1342 99956 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.446→44.216 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4633 0 21 792 5446
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034760
X-RAY DIFFRACTIONf_angle_d0.6116411
X-RAY DIFFRACTIONf_dihedral_angle_d17.1021809
X-RAY DIFFRACTIONf_chiral_restr0.055750
X-RAY DIFFRACTIONf_plane_restr0.003831
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4461-1.46250.21551450.14932659X-RAY DIFFRACTION84
1.4625-1.47970.21341650.13973105X-RAY DIFFRACTION100
1.4797-1.49780.20981760.13443208X-RAY DIFFRACTION100
1.4978-1.51670.19731710.12373211X-RAY DIFFRACTION100
1.5167-1.53670.19121580.1293118X-RAY DIFFRACTION100
1.5367-1.55780.20331500.1223211X-RAY DIFFRACTION100
1.5578-1.580.18581450.12043248X-RAY DIFFRACTION100
1.58-1.60360.18111480.12143104X-RAY DIFFRACTION100
1.6036-1.62870.17341330.12493223X-RAY DIFFRACTION100
1.6287-1.65540.17021540.1253232X-RAY DIFFRACTION100
1.6554-1.68390.20771600.1253150X-RAY DIFFRACTION100
1.6839-1.71450.171660.12833186X-RAY DIFFRACTION100
1.7145-1.74750.18831630.12943199X-RAY DIFFRACTION100
1.7475-1.78320.17191670.1293156X-RAY DIFFRACTION100
1.7832-1.82190.17721700.13133222X-RAY DIFFRACTION100
1.8219-1.86430.2061560.13843127X-RAY DIFFRACTION100
1.8643-1.9110.1741480.13683253X-RAY DIFFRACTION100
1.911-1.96260.17781590.13193148X-RAY DIFFRACTION100
1.9626-2.02040.19551450.13533221X-RAY DIFFRACTION100
2.0204-2.08560.19171760.13283169X-RAY DIFFRACTION100
2.0856-2.16010.20831930.12873193X-RAY DIFFRACTION100
2.1601-2.24660.181990.12273145X-RAY DIFFRACTION100
2.2466-2.34890.15671830.12713160X-RAY DIFFRACTION100
2.3489-2.47270.16831520.12813235X-RAY DIFFRACTION100
2.4727-2.62760.15561420.12613210X-RAY DIFFRACTION100
2.6276-2.83040.17551410.13473211X-RAY DIFFRACTION100
2.8304-3.11520.2021740.13753219X-RAY DIFFRACTION100
3.1152-3.56580.15791570.12923222X-RAY DIFFRACTION100
3.5658-4.49180.15361780.12073214X-RAY DIFFRACTION100
4.4918-44.23680.18261380.16083187X-RAY DIFFRACTION96

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