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- PDB-2q9a: Structure of Apo FTSY -

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Basic information

Entry
Database: PDB / ID: 2q9a
TitleStructure of Apo FTSY
ComponentsCell division protein ftsY
KeywordsSIGNALING PROTEIN / INNER MEMBRANE / RIBONUCLEOPROTEIN / NUCLEOTIDE-BINDING / SIGNAL RECOGNITION PARTICLE / SRP / GDP / FFH / FTSY / GTPASE / RNA-BINDING / GTP-BINDING / CELL DIVISION / MEMBRANE / CELL CYCLE
Function / homology
Function and homology information


signal-recognition-particle GTPase / SRP-dependent cotranslational protein targeting to membrane / GTPase activity / GTP binding / ATP hydrolysis activity / plasma membrane / cytoplasm
Similarity search - Function
SRP54, nucleotide-binding 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, nucleotide-binding 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 / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Signal recognition particle receptor FtsY
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.24 Å
AuthorsReyes, C.L. / Stroud, R.M.
CitationJournal: Plos One / Year: 2007
Title: X-ray Structures of the Signal Recognition Particle Receptor Reveal Targeting Cycle Intermediates.
Authors: Reyes, C.L. / Rutenber, E. / Walter, P. / Stroud, R.M.
History
DepositionJun 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell division protein ftsY
B: Cell division protein ftsY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,63020
Polymers66,2072
Non-polymers1,42318
Water7,044391
1
A: Cell division protein ftsY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,95612
Polymers33,1031
Non-polymers85311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Cell division protein ftsY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6748
Polymers33,1031
Non-polymers5707
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-115 kcal/mol
Surface area25850 Å2
MethodPISA
4
B: Cell division protein ftsY
hetero molecules

A: Cell division protein ftsY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,63020
Polymers66,2072
Non-polymers1,42318
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+3/2,-y+1,z+1/21
Buried area4060 Å2
ΔGint-103 kcal/mol
Surface area26940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.627, 96.683, 99.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cell division protein ftsY / / FTSY


Mass: 33103.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Gene: ftsY / Plasmid: PET-28B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) ROSETTA / References: UniProt: P83749
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 391 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.79 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.24→19.7 Å / Num. obs: 29767 / Biso Wilson estimate: 19.4 Å2

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Processing

SoftwareName: CNS / Version: 1.2 / Classification: refinement
RefinementResolution: 2.24→19.7 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1789223.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.247 2839 9.5 %RANDOM
Rwork0.223 ---
obs0.223 29767 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.6346 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 29.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20 Å20 Å2
2---4.71 Å20 Å2
3---3.99 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.24→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4536 0 81 391 5008
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.021
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.51
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it11.5
X-RAY DIFFRACTIONc_mcangle_it1.392
X-RAY DIFFRACTIONc_scbond_it2.612
X-RAY DIFFRACTIONc_scangle_it3.222.5
LS refinement shellHighest resolution: 2.24 Å / Total num. of bins used: 6
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3edo.paramedo.top
X-RAY DIFFRACTION5ion.paramion.top

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