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- PDB-6cy1: Crystal structure of Signal recognition particle receptor FtsY fr... -

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Basic information

Entry
Database: PDB / ID: 6cy1
TitleCrystal structure of Signal recognition particle receptor FtsY from Elizabethkingia anophelis
ComponentsSignal recognition particle receptor FtsY
KeywordsSIGNALING PROTEIN / Signal recognition particle receptor FtsY / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


SRP-dependent cotranslational protein targeting to membrane / GTPase activity / GTP binding / plasma membrane / cytoplasm
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 speciesElizabethkingia anophelis NUHP1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of Signal recognition particle receptor FtsY from Elizabethkingia anophelis
Authors: Delker, S.L. / Abendroth, J. / Lorimer, D. / Edwards, T.E.
History
DepositionApr 4, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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)72,6614
Polymers72,5032
Non-polymers1582
Water6,557364
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-17 kcal/mol
Surface area24420 Å2
Unit cell
Length a, b, c (Å)70.800, 70.800, 229.050
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 0 through 17 or (resid 18...
21(chain B and (resid 0 through 10 or (resid 11...

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
11METMETASPASP(chain A and (resid 0 through 17 or (resid 18...AA0 - 179 - 26
12LYSLYSLYSLYS(chain A and (resid 0 through 17 or (resid 18...AA1827
13HISHISLYSLYS(chain A and (resid 0 through 17 or (resid 18...AA-3 - 3166 - 325
14HISHISLYSLYS(chain A and (resid 0 through 17 or (resid 18...AA-3 - 3166 - 325
15HISHISLYSLYS(chain A and (resid 0 through 17 or (resid 18...AA-3 - 3166 - 325
16HISHISLYSLYS(chain A and (resid 0 through 17 or (resid 18...AA-3 - 3166 - 325
21METMETLYSLYS(chain B and (resid 0 through 10 or (resid 11...BB0 - 109 - 19
22GLUGLUGLUGLU(chain B and (resid 0 through 10 or (resid 11...BB1120
23METMETLYSLYS(chain B and (resid 0 through 10 or (resid 11...BB0 - 3159 - 324
24METMETLYSLYS(chain B and (resid 0 through 10 or (resid 11...BB0 - 3159 - 324
25METMETLYSLYS(chain B and (resid 0 through 10 or (resid 11...BB0 - 3159 - 324
26METMETLYSLYS(chain B and (resid 0 through 10 or (resid 11...BB0 - 3159 - 324

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Components

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


Mass: 36251.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Elizabethkingia anophelis NUHP1 (bacteria)
Gene: ftsY, BD94_0405 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A077EFA5
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / 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: 2.37 Å3/Da / Density % sol: 48.04 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.7
Details: tray 291453 B12: JCSG+ : 200 mM Potassium citrate tribasic, 20% (w/v) PEG 3350: Cryo = 20%EG : ElanA.00983.a.B1 at 20 mg/ml, puck drh8-9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 18, 2017 / Details: mirrors
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.9→41.85 Å / Num. obs: 51029 / % possible obs: 100 % / Redundancy: 9.633 % / Biso Wilson estimate: 29.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rrim(I) all: 0.068 / Χ2: 1.008 / Net I/σ(I): 21.02 / Num. measured all: 491587
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.9-1.959.60.564.0136491380138010.9070.591100
1.95-29.6020.4315.2234988364436440.9420.455100
2-2.069.6210.3416.6234241355935590.9630.36100
2.06-2.129.6280.2638.533506348034800.980.277100
2.12-2.199.6470.19911.0832509337033700.9870.21100
2.19-2.279.6520.16213.4431341324732470.9910.171100
2.27-2.369.6440.13515.8930272313931390.9940.142100
2.36-2.459.6750.1217.8229403303930390.9950.127100
2.45-2.569.6690.10819.727759287128710.9950.114100
2.56-2.699.6770.09222.5826717276127610.9970.097100
2.69-2.839.6770.07926.0325829266926690.9970.083100
2.83-39.6690.06630.4323815246324630.9980.07100
3-3.219.6670.05734.3922833236223620.9980.06100
3.21-3.479.6260.05238.420811216221620.9980.055100
3.47-3.89.6490.04741.219404201120110.9990.049100
3.8-4.259.6540.04544.0817571182018200.9990.047100
4.25-4.919.660.04345.7815611161616160.9980.046100
4.91-6.019.5840.04544.5513121136913690.9990.048100
6.01-8.59.5390.04245.1210026105110510.9990.044100
8.5-41.858.9730.04245.553396055950.9990.04498.3

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→41.85 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.91
RfactorNum. reflection% reflection
Rfree0.1997 2007 3.94 %
Rwork0.1718 --
obs0.173 50922 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 122.52 Å2 / Biso mean: 39.5183 Å2 / Biso min: 14.45 Å2
Refinement stepCycle: final / Resolution: 1.9→41.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4623 0 9 368 5000
Biso mean--71.69 43.84 -
Num. residues----621
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2512X-RAY DIFFRACTION8.197TORSIONAL
12B2512X-RAY DIFFRACTION8.197TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9-1.94750.28341450.219635053650
1.9475-2.00020.29321320.205734803612
2.0002-2.0590.21911420.196534933635
2.059-2.12550.22761320.185435003632
2.1255-2.20140.20071700.179234793649
2.2014-2.28960.22921370.179735003637
2.2896-2.39380.21971190.180634963615
2.3938-2.520.23211520.183934923644
2.52-2.67780.22051580.191434683626
2.6778-2.88450.2041430.192434883631
2.8845-3.17470.23991440.180935073651
3.1747-3.63390.21161380.16934953633
3.6339-4.57740.14581410.142735043645
4.5774-41.86010.171540.15935083662
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)
12.1128-0.94460.70981.336-0.31440.91430.0470.049-0.1605-0.02450.0210.32440.059-0.0549-0.06950.18940.00770.01250.2527-0.04140.2074-12.706-18.6587-5.9866
23.34780.1630.00362.2839-0.37351.86370.06120.3680.17470.0308-0.0283-0.2445-0.17390.1461-0.03680.1587-0.0028-0.01250.2574-0.01740.161820.4516-15.35852.9336
32.685-0.44281.21931.5814-0.39521.82-0.0570.05360.09720.0633-0.01580.0163-0.15140.07840.06440.15480.02790.00030.2549-0.03610.1474-0.3167-15.461-1.5997
41.9718-0.00750.47161.3498-0.41841.80830.0755-0.0983-0.2320.45310.1845-1.00310.15040.448-0.18220.5080.0263-0.25830.421-0.19960.749-0.18279.61089.7289
52.8614-0.23821.29393.25380.59011.3910.1002-0.095-0.20810.01390.02440.0583-0.0382-0.0476-0.08950.2341-0.0030.02360.2107-0.05760.2321-25.37812.2696-5.1149
62.9551-1.9274-0.58484.01440.512.91320.24880.11130.0017-0.5441-0.30160.2331-0.0144-0.05910.05680.34160.0011-0.01260.2145-0.05840.2175-26.50110.9194-17.8933
72.5498-0.48851.17623.6066-0.03361.4730.06470.0243-0.19760.13840.2041-0.53390.12580.2084-0.23120.22810.0351-0.05030.2565-0.13850.3351-13.19069.2332-0.715
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -3 through 124 )A-3 - 124
2X-RAY DIFFRACTION2chain 'A' and (resid 125 through 234 )A125 - 234
3X-RAY DIFFRACTION3chain 'A' and (resid 235 through 316 )A235 - 316
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 81 )B0 - 81
5X-RAY DIFFRACTION5chain 'B' and (resid 82 through 194 )B82 - 194
6X-RAY DIFFRACTION6chain 'B' and (resid 195 through 234 )B195 - 234
7X-RAY DIFFRACTION7chain 'B' and (resid 235 through 315 )B235 - 315

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