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- PDB-6fqd: Escherichia Coli Signal Recognition Particle Receptor FtsY NGdN1 -

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Basic information

Entry
Database: PDB / ID: 6fqd
TitleEscherichia Coli Signal Recognition Particle Receptor FtsY NGdN1
ComponentsSignal recognition particle receptor FtsY
KeywordsSIGNALING PROTEIN / FtsY / SRP / SRP-Receptor / Protein Translocation
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
GUANOSINE-5'-DIPHOSPHATE / : / Signal recognition particle receptor FtsY
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.10000574506 Å
AuthorsMrusek, D.
Funding support Israel, Germany, 4items
OrganizationGrant numberCountry
Israel Science FoundationISF 600/11 Israel
German Research FoundationINST160/621-1FUGG Germany
German Research FoundationBA 5311/6-1 Germany
German Research FoundationCRC-TRR174 Germany
CitationJournal: J. Mol. Biol. / Year: 2018
Title: Co-translational Folding Intermediate Dictates Membrane Targeting of the Signal Recognition Particle Receptor.
Authors: Karniel, A. / Mrusek, D. / Steinchen, W. / Dym, O. / Bange, G. / Bibi, E.
History
DepositionFeb 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 17, 2024Group: 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 / struct_ncs_dom_lim
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)63,4326
Polymers62,4682
Non-polymers9654
Water5,891327
1
A: Signal recognition particle receptor FtsY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7163
Polymers31,2341
Non-polymers4822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Signal recognition particle receptor FtsY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7163
Polymers31,2341
Non-polymers4822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)110.963, 110.963, 110.632
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSGLYGLY(chain 'A' and (resid 221 through 489 or resid 491 through 493))AA221 - 2559 - 43
12ASPASPILEILE(chain 'A' and (resid 221 through 489 or resid 491 through 493))AA263 - 48951 - 277
13ALAALAPHEPHE(chain 'A' and (resid 221 through 489 or resid 491 through 493))AA491 - 493279 - 281
24LYSLYSGLYGLY(chain 'B' and (resid 221 through 256 or resid 263 through 489 or resid 491 through 493))BB221 - 2559 - 43
25ASPASPILEILE(chain 'B' and (resid 221 through 256 or resid 263 through 489 or resid 491 through 493))BB263 - 48951 - 277
26ALAALAPHEPHE(chain 'B' and (resid 221 through 256 or resid 263 through 489 or resid 491 through 493))BB491 - 493279 - 281

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Components

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


Mass: 31233.758 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 (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P10121
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 2.84 Å3/Da / Density % sol: 56.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1 M Na-citrate pH 5.6, 20% isopropanol, 20% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 15, 2017
RadiationMonochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→45.28 Å / Num. obs: 38419 / % possible obs: 98.28 % / Redundancy: 3.9 % / Biso Wilson estimate: 32.5 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.08104 / Rpim(I) all: 0.04482 / Rrim(I) all: 0.09318 / Net I/σ(I): 10.34
Reflection shellResolution: 2.1→2.175 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.4298 / Mean I/σ(I) obs: 2.64 / Num. unique obs: 3856 / CC1/2: 0.786 / Rpim(I) all: 0.2529 / Rrim(I) all: 0.5026 / % possible all: 98.32

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Processing

Software
NameVersionClassification
PHENIX1.12rc0_2798refinement
PHASER1.10.1_2155phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FTS

1fts


Resolution: 2.10000574506→45.2778491151 Å / SU ML: 0.209616798714 / Cross valid method: FREE R-VALUE / σ(F): 1.37329835597 / Phase error: 19.5573445909
RfactorNum. reflection% reflection
Rfree0.208330514311 2051 5.33919925027 %
Rwork0.177498663372 --
obs0.179084479123 38414 98.288258322 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 45.0229960901 Å2
Refinement stepCycle: LAST / Resolution: 2.10000574506→45.2778491151 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4098 0 58 327 4483
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004503189311134204
X-RAY DIFFRACTIONf_angle_d0.8063201948445684
X-RAY DIFFRACTIONf_chiral_restr0.0456848001213675
X-RAY DIFFRACTIONf_plane_restr0.00381718099437727
X-RAY DIFFRACTIONf_dihedral_angle_d11.17280186452528
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.14890.2851006686211100.2334098428152417X-RAY DIFFRACTION97.6807112486
2.1489-2.20260.2556673618231350.2156906125752450X-RAY DIFFRACTION99.8455001931
2.2026-2.26210.2314437640941530.211134386252448X-RAY DIFFRACTION99.4646271511
2.2621-2.32870.2532160633071280.1965397943772445X-RAY DIFFRACTION99.5357833656
2.3287-2.40390.240258668061330.1961180879572464X-RAY DIFFRACTION99.5019157088
2.4039-2.48980.2074195345731530.1881167274722411X-RAY DIFFRACTION98.9579313007
2.4898-2.58950.2436541269171450.1908408921212378X-RAY DIFFRACTION97.3755306831
2.5895-2.70730.2085831965811580.1917401695712417X-RAY DIFFRACTION98.7725354814
2.7073-2.850.248136352091900.1886774807292367X-RAY DIFFRACTION98.9551083591
2.85-3.02850.2171688880521270.1858614829262449X-RAY DIFFRACTION98.7351475661
3.0285-3.26230.1883706847341320.1821214450012424X-RAY DIFFRACTION97.9310344828
3.2623-3.59050.2017995362761060.1674942933112393X-RAY DIFFRACTION96.7479674797
3.5905-4.10970.1728172250951330.1549576367482449X-RAY DIFFRACTION98.1375902699
4.1097-5.17660.180740413881110.1547294883272416X-RAY DIFFRACTION96.968534152
5.1766-45.28840.2033085509811370.1757287988532435X-RAY DIFFRACTION95.9343528534
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)
12.070702585590.7139611314950.5292131214081.29766962198-0.6960072795810.869056523431-0.0283252021459-0.495083758230.2633840026690.2984371589970.256058030123-0.612239927682-0.4884830952780.3886895850180.1874006500260.519509932422-0.250997659585-0.04580087723860.505767966249-0.137997116960.54282694529241.280046933923.64763235194.10621691973
21.32954571533-0.03029335504920.4771056960081.54034161195-0.266007529081.593233816690.04774748732060.2819185406210.0728610198496-0.418199612657-0.0692755939256-0.0992446559274-0.1414562164180.08340430961780.01236215847320.2891276989170.006788181184040.09535281785130.275016807508-0.02555224275890.24762520369326.56132884732.35140033594-19.5437731136
31.47362567477-0.168882905754-0.2072451957762.136062332340.08645470196721.725838177490.1545308737590.10429900706-0.02747857589090.0943736758038-0.204348569681-0.4441385084140.02014818074020.245121611456-0.05871527148170.202676789707-0.03481871345990.04257744820970.283175084233-0.03491724009510.25125531857133.44580533540.338335276707-13.2739378544
42.973788762970.02469790364840.6466221059831.004875287920.2013309355042.229678061520.009685507660610.1363852298750.742431612397-0.109682769515-0.181923259229-0.377464235618-0.4475844093910.329441568910.04379668513620.284981828219-0.04223323876990.04320666855050.2934011506940.01991516031470.47970543630826.020117466117.9333699072-13.0584017199
51.86807273306-2.04016108554-0.4094835842332.687062302780.7552124010730.8650801577480.06648731664770.188792331781-0.140566226765-0.5948662935720.166456118665-0.2959197146770.07354489075990.479038943654-0.03083465206420.3007111562350.06061616035160.08836794603770.566426675732-0.1066799798040.57799186978945.3780168195-12.1472462821-1.01118033196
64.76765026406-4.762284876210.1377059445564.89752815584-0.3838017019870.498753908865-0.00717457505261-0.00489163238101-0.0707487378788-0.2274162319230.282541239115-0.636223404256-0.002729931983980.3184641751560.1693786396870.2014863244190.0391023465128-0.01738225577740.650641523741-0.06844168910130.6827864007649.5145439687-6.125122870715.0877557497
71.99672291543-0.260701053018-0.4738076147751.417482883120.5028812938221.26001446327-0.0756691814647-0.2232743316480.05216637716990.1274667704780.0530640864962-0.0630831184412-0.02520206184580.171490484231-0.01106048274390.212808983129-0.0381034907178-0.08758551890510.288193927023-0.00239813804630.23734322428227.26092797089.9829356817222.803386888
80.7823266789840.272375165087-0.2399369802611.40452690915-0.1276856992091.46848115792-0.0132982528294-0.0215853594324-0.651946565831-0.326172117929-0.0548611083522-0.6434735432170.4881070434670.563889334919-0.05965568352930.2347954194240.0498191049877-0.02535439520930.4070387696970.02456235393210.46083296710633.9302426012-2.7066111846618.2362510185
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 221 through 263 )
2X-RAY DIFFRACTION2chain 'A' and (resid 264 through 373 )
3X-RAY DIFFRACTION3chain 'A' and (resid 374 through 472 )
4X-RAY DIFFRACTION4chain 'A' and (resid 473 through 494 )
5X-RAY DIFFRACTION5chain 'B' and (resid 221 through 237 )
6X-RAY DIFFRACTION6chain 'B' and (resid 238 through 263 )
7X-RAY DIFFRACTION7chain 'B' and (resid 264 through 454 )
8X-RAY DIFFRACTION8chain 'B' and (resid 455 through 493 )

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