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- PDB-6cy5: Crystal structure of Signal recognition particle receptor FtsY fr... -

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Basic information

Entry
Database: PDB / ID: 6cy5
TitleCrystal structure of Signal recognition particle receptor FtsY from Elizabethkingia anophelis in complex with GDP
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


signal recognition particle binding / signal-recognition-particle GTPase / SRP-dependent cotranslational protein targeting to membrane / GTPase activity / GTP binding / ATP hydrolysis activity / metal ion binding / plasma membrane / cytoplasm
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 speciesElizabethkingia anophelis NUHP1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 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 in complex with GDP
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 1.1Jan 15, 2020Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.2Mar 13, 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_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

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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)74,37815
Polymers72,5032
Non-polymers1,87513
Water12,989721
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-15 kcal/mol
Surface area27100 Å2
Unit cell
Length a, b, c (Å)49.520, 49.640, 69.710
Angle α, β, γ (deg.)101.180, 99.100, 105.580
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 1 and (name N or name...
21(chain B and (resid 1 through 11 or (resid 12...

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
11METMETMETMET(chain A and ((resid 1 and (name N or name...AA19
12METMETARGARG(chain A and ((resid 1 and (name N or name...AA1 - 3189 - 326
13METMETARGARG(chain A and ((resid 1 and (name N or name...AA1 - 3189 - 326
14METMETARGARG(chain A and ((resid 1 and (name N or name...AA1 - 3189 - 326
15METMETARGARG(chain A and ((resid 1 and (name N or name...AA1 - 3189 - 326
21METMETLYSLYS(chain B and (resid 1 through 11 or (resid 12...BB1 - 119 - 19
22GLUGLUGLUGLU(chain B and (resid 1 through 11 or (resid 12...BB1220
23METMETARGARG(chain B and (resid 1 through 11 or (resid 12...BB1 - 3189 - 326
24METMETARGARG(chain B and (resid 1 through 11 or (resid 12...BB1 - 3189 - 326
25METMETARGARG(chain B and (resid 1 through 11 or (resid 12...BB1 - 3189 - 326

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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-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 721 / 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: 2.26 Å3/Da / Density % sol: 45.5 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.7
Details: tray 291448 H10: MCSG1: 0.1 M HEPES: NaOH, pH 7.5 25 % (w/v) PEG 3350 +4mM GTP/MgCl2: Cryo = 15%EG : ElanA.00983.a.B1 at 20 mg/ml, puck frp4-2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 0.9787 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Sep 29, 2017 / Details: mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.7→43.43 Å / Num. obs: 66029 / % possible obs: 98 % / Redundancy: 7.105 % / Biso Wilson estimate: 14.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rrim(I) all: 0.052 / Χ2: 1.022 / Net I/σ(I): 25.34 / Num. measured all: 469119 / Scaling rejects: 1000
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.7-1.743.2580.2434.1143910.9440.28788.3
1.74-1.794.5410.2245.6245710.9640.25193.7
1.79-1.844.7050.1796.9745110.9790.295.3
1.84-1.94.8170.158.5245050.9870.16797.6
1.9-1.964.9630.12210.7143580.9910.13599.1
1.96-2.035.1250.10313.3143000.9930.11499.9
2.03-2.115.4220.08816.7841290.9950.09899.8
2.11-2.196.4710.07321.7339980.9970.0899.8
2.19-2.297.1020.06425.9138160.9980.06999.9
2.29-2.47.610.0628.9936860.9980.06599.9
2.4-2.538.1240.05830.5234540.9980.06299.9
2.53-2.698.9250.05434.0332870.9990.05799.9
2.69-2.8710.5480.05140.3331170.9990.054100
2.87-3.111.1840.04745.8428800.9990.04999.6
3.1-3.411.1550.04350.826270.9990.045100
3.4-3.811.0630.03956.6923970.9990.0499.7
3.8-4.3911.0070.03659.1720990.9990.03899.7
4.39-5.3811.0340.03759.2717790.9990.03999.5
5.38-7.611.0710.04153.3413720.9990.04399.4
7.6-43.4310.410.03761.647520.9990.03899.3

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→43.43 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 18.67
RfactorNum. reflection% reflection
Rfree0.1936 1974 2.99 %
Rwork0.157 --
obs0.158 66024 98.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 78.91 Å2 / Biso mean: 21.293 Å2 / Biso min: 5.79 Å2
Refinement stepCycle: final / Resolution: 1.7→43.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4745 0 146 742 5633
Biso mean--23.17 31.99 -
Num. residues----634
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2802X-RAY DIFFRACTION3.732TORSIONAL
12B2802X-RAY DIFFRACTION3.732TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.74250.27591400.19724089422988
1.7425-1.78970.18591260.18254390451694
1.7897-1.84230.24711370.17674476461396
1.8423-1.90180.25831320.18164551468397
1.9018-1.96980.21121460.16514628477499
1.9698-2.04860.17071610.155546254786100
2.0486-2.14190.18771550.152646654820100
2.1419-2.25480.18021180.148247024820100
2.2548-2.3960.20161150.146346694784100
2.396-2.5810.20421450.16246574802100
2.581-2.84070.19021550.160246214776100
2.8407-3.25160.20551430.161246694812100
3.2516-4.09620.16251550.140446754830100
4.0962-43.44410.18981460.154546334779100
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)
12.4426-0.8427-0.20361.8560.11711.0679-0.0793-0.2432-0.18250.25490.0988-0.03170.10560.03080.00330.1359-0.0132-0.03250.1180.03170.09864.3506-8.25520.1393
22.208-0.92480.08591.3167-0.22830.4401-0.1039-0.1910.01980.14570.0746-0.0327-0.04940.01060.01280.1187-0.02870.00910.0876-0.00820.0648-5.39264.824616.1671
32.1361-0.419-1.22011.2922-0.16171.859-0.00580.10890.1819-0.04350.00810.0589-0.1424-0.1029-0.0190.10980.0024-0.02430.08260.00780.108-17.470619.57954.3021
42.4147-1.26790.17441.66630.08371.7350.0707-0.0322-0.01210.0496-0.03610.0210.06680.009-0.02570.07-0.0124-0.00560.0628-0.00210.0664-3.58982.858113.7581
53.15-0.0950.10982.29590.5350.9318-0.06850.7378-0.4217-0.53520.0142-0.02590.06810.1439-0.02060.27730.0121-0.02410.2495-0.03050.18468.6657-12.4832-26.246
62.1124-0.83260.29742.2263-0.1411.44420.07540.0689-0.0799-0.11630.00860.4466-0.036-0.3032-0.01720.1136-0.0009-0.03460.14830.01710.1677-8.84982.2717-16.1188
72.8477-1.22881.18793.0545-1.17463.2951-0.07940.42540.3964-0.3169-0.0764-0.1098-0.20610.07550.06630.2003-0.0123-0.00780.15040.01770.18940.554211.4439-21.383
81.6533-1.23250.43951.9113-0.26380.60350.13280.27470.0684-0.2495-0.1444-0.0484-0.00560.0734-0.00380.1251-0.00790.00540.13270.0010.089813.1579-7.4685-18.9647
92.59310.54650.13532.25330.27441.61390.1103-0.1614-0.19750.26-0.08560.01030.18030.0605-0.02480.12160.00410.00390.07710.02540.135925.6769-24.5857-4.4252
102.0727-0.5546-0.97151.31151.1562.92030.0303-0.03010.0848-0.01320.0111-0.2428-0.09870.1794-0.03710.088-0.0002-0.02390.09060.01390.120829.2711-12.4765-4.0525
112.0993-1.3469-0.13651.7127-0.33721.4743-00.0374-0.0004-0.07320.02970.02040.012-0.0551-0.02960.0759-0.0072-0.00990.0683-0.0020.073510.316-7.7999-13.3245
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 60 )A1 - 60
2X-RAY DIFFRACTION2chain 'A' and (resid 61 through 169 )A61 - 169
3X-RAY DIFFRACTION3chain 'A' and (resid 170 through 235 )A170 - 235
4X-RAY DIFFRACTION4chain 'A' and (resid 236 through 318 )A236 - 318
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 21 )B1 - 21
6X-RAY DIFFRACTION6chain 'B' and (resid 22 through 60 )B22 - 60
7X-RAY DIFFRACTION7chain 'B' and (resid 61 through 78 )B61 - 78
8X-RAY DIFFRACTION8chain 'B' and (resid 79 through 141 )B79 - 141
9X-RAY DIFFRACTION9chain 'B' and (resid 142 through 195 )B142 - 195
10X-RAY DIFFRACTION10chain 'B' and (resid 196 through 235 )B196 - 235
11X-RAY DIFFRACTION11chain 'B' and (resid 236 through 318 )B236 - 318

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