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- PDB-6dlx: FtsY-NG domain bound to fragment 3. -

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Basic information

Entry
Database: PDB / ID: 6dlx
TitleFtsY-NG domain bound to fragment 3.
ComponentsSignal recognition particle receptor FtsY
KeywordsSIGNALING PROTEIN / SRP / SR receptor / FtsY / FBDD
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
4-bromo-2,5-dimethoxyaniline / AMMONIUM ION / DI(HYDROXYETHYL)ETHER / : / Signal recognition particle receptor FtsY
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.848 Å
AuthorsAtaide, F.S. / Faoro, C.
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
DepositionJun 4, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 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)67,54324
Polymers66,2022
Non-polymers1,34122
Water4,378243
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint19 kcal/mol
Surface area25570 Å2
Unit cell
Length a, b, c (Å)34.451, 76.020, 107.882
Angle α, β, γ (deg.)90.00, 90.41, 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 (E. coli) / Gene: ftsY, BK409_14805
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A1M2TDP9, UniProt: P10121*PLUS
#2: Chemical
ChemComp-GXY / 4-bromo-2,5-dimethoxyaniline


Mass: 232.074 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10BrNO2
#3: Chemical
ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: H4N
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.15 Å3/Da / Density % sol: 42.86 %
Crystal growTemperature: 297.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis-Tris pH 5.8, 25% PEG 3350, 165 mM ammonium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.848→43.991 Å / Num. obs: 47444 / % possible obs: 99.36 % / Redundancy: 2 % / Biso Wilson estimate: 27.3 Å2 / Rmerge(I) obs: 0.028 / Rpim(I) all: 0.02828 / Rrim(I) all: 0.04 / Net I/σ(I): 13.8
Reflection shellResolution: 1.848→1.914 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: 1.848→43.991 Å / Cross valid method: FREE R-VALUE / σ(F): 7.52 / Phase error: 36.33
RfactorNum. reflection% reflection
Rfree0.2493 2331 4.95 %
Rwork0.2 --
obs0.2051 47444 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.848→43.991 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4594 0 72 243 4909
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034725
X-RAY DIFFRACTIONf_angle_d0.5536360
X-RAY DIFFRACTIONf_dihedral_angle_d14.0952882
X-RAY DIFFRACTIONf_chiral_restr0.038740
X-RAY DIFFRACTIONf_plane_restr0.004818
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8496-1.88740.33041450.32732615X-RAY DIFFRACTION94
1.8874-1.92840.37831330.32262619X-RAY DIFFRACTION94
1.9284-1.97320.35911270.28542642X-RAY DIFFRACTION95
1.9732-2.02250.2881510.28172646X-RAY DIFFRACTION94
2.0225-2.07720.33641020.27612623X-RAY DIFFRACTION96
2.0772-2.13830.27431400.26392691X-RAY DIFFRACTION95
2.1383-2.20730.31931160.24852607X-RAY DIFFRACTION95
2.2073-2.28610.25431380.25332666X-RAY DIFFRACTION95
2.2861-2.37760.28791280.24672632X-RAY DIFFRACTION95
2.3776-2.48570.29181380.23532669X-RAY DIFFRACTION95
2.4857-2.61660.30381320.23362673X-RAY DIFFRACTION95
2.6166-2.78040.29791140.22352660X-RAY DIFFRACTION96
2.7804-2.99470.24231540.21752646X-RAY DIFFRACTION94
2.9947-3.29550.24891580.19752634X-RAY DIFFRACTION94
3.2955-3.77090.22451620.16492663X-RAY DIFFRACTION94
3.7709-4.74560.19021140.13152698X-RAY DIFFRACTION96
4.7456-24.96840.22751790.16142689X-RAY DIFFRACTION93
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)
10.14830.0416-0.02750.54910.01460.105-0.0103-0.0138-0.0571-0.1464-0.0381-0.0225-0.027-0.008-0.090.42970.0023-0.0510.03280.01330.233547.8503-11.2538.7191
20.538-0.41190.00891.31380.15030.0383-0.0227-0.06820.12030.25650.02260.0889-0.0582-0.0162-0.05070.36240.0039-0.03610.0664-0.00890.213845.8034.550843.4728
30.43230.073-0.13571.08670.26960.12140.0096-0.0067-0.0442-0.0216-0.0168-0.05730.05850.0133-0.00550.31950.0103-0.05340.0629-0.02780.215148.4189-13.394737.038
40.1032-0.19310.05061.0188-0.21420.2691-0.04580.01790.11030.0441-0.01230.1052-0.1123-0.0132-0.01480.46060.0248-0.02480.09020.02030.285524.7911-10.81911.36
50.2746-0.07570.04170.65150.1580.54130.07690.0141-0.1124-0.0368-0.0110.0189-0.02760.0673-0.01410.29660.00310.00630.08240.00030.226239.0253-46.908918.7508
60.70250.06510.18341.44820.2830.3442-0.03040.0928-0.0338-0.3159-0.00560.09820.0052-0.0120.04430.3389-0.0098-0.01330.0560.00170.267829.7313-50.051912.9324
70.4242-0.3385-0.08971.3244-0.10560.04880.01330.0124-0.0175-0.0294-0.01250.0557-0.07960.01230.02520.3652-0.0091-0.0110.06780.0080.220431.5946-29.154714.2792
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 195 through 373 )
2X-RAY DIFFRACTION2chain 'A' and (resid 374 through 438 )
3X-RAY DIFFRACTION3chain 'A' and (resid 439 through 494 )
4X-RAY DIFFRACTION4chain 'B' and (resid 195 through 282 )
5X-RAY DIFFRACTION5chain 'B' and (resid 283 through 373 )
6X-RAY DIFFRACTION6chain 'B' and (resid 374 through 413 )
7X-RAY DIFFRACTION7chain 'B' and (resid 414 through 494 )

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