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- PDB-2iyl: Structure of an FtsY:GDP complex -

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Basic information

Entry
Database: PDB / ID: 2iyl
TitleStructure of an FtsY:GDP complex
ComponentsCELL DIVISION PROTEIN FTSY
KeywordsCELL CYCLE / INNER MEMBRANE / RIBONUCLEOPROTEIN / NUCLEOTIDE-BINDING / SIGNAL RECOGNITION PARTICLE / SRP / GDP / FFH / FTSY / GTPASE / RNA-BINDING / GTP-BINDING / CELL DIVISION / MEMBRANE
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
GUANOSINE-5'-DIPHOSPHATE / Signal recognition particle receptor FtsY
Similarity search - Component
Biological speciesTHERMUS AQUATICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsFocia, P.J. / Freymann, D.M.
CitationJournal: Proteins / Year: 2007
Title: X-ray structure of the T. aquaticus FtsY:GDP complex suggests functional roles for the C-terminal helix of the SRP GTPases.
Authors: Gawronski-Salerno, J. / Coon 5th., J.S. / Focia, P.J. / Freymann, D.M.
History
DepositionJul 18, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 2, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 19, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Source and taxonomy
Category: atom_site / citation ...atom_site / citation / citation_author / entity_src_gen / struct_conn
Item: _atom_site.label_alt_id / _citation.journal_id_ISSN ..._atom_site.label_alt_id / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: CELL DIVISION PROTEIN FTSY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4004
Polymers30,7651
Non-polymers6353
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)105.196, 105.196, 54.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein CELL DIVISION PROTEIN FTSY / / FTSY


Mass: 30764.586 Da / Num. of mol.: 1 / Fragment: NGD20, RESIDUES 20-303
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS AQUATICUS (bacteria) / Plasmid: PJGS3 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): ROSETTA-2 pLysS / References: UniProt: P83749
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 2-20 DELETED IN THE FTSY NG DOMAIN EXPRESSION CONSTRUCT FTSY NGD20. MET 1 NOT PRESENT.

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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: 2.39 Å3/Da / Density % sol: 48.06 %
Description: CHAIN D OF ENTRY 1OKK, THE FTSY NG DOMAIN IN ITS HETERODIMERIC COMPLEX WITH FFH NG, WAS USED FOR MOLECULAR REPLACEMENT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 17, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.06→48.39 Å / Num. obs: 136283 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 20.1
Reflection shellResolution: 2.06→2.17 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OKK

1okk


Resolution: 2.1→11.87 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.878 / SU B: 5.455 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.244 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE OMITTED FROM THE MODEL. THESE INCLUDE RESIDUES 80-82, 95-96, 141-146, AND 235- 236. THREE GLUTAMATE SIDECHAINS, ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE OMITTED FROM THE MODEL. THESE INCLUDE RESIDUES 80-82, 95-96, 141-146, AND 235- 236. THREE GLUTAMATE SIDECHAINS, D70, D151, AND D295, EXHIBIT EVIDENCE OF RADIATION DAMAGE AND THEIR CARBOXYLATE GROUP CD- OE1-OE2 ATOMS ARE MODELED AT 0.5 OCCUPANCY.
RfactorNum. reflection% reflectionSelection details
Rfree0.291 895 5.2 %RANDOM
Rwork0.207 ---
obs0.211 16465 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.96 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.1→11.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2063 0 38 144 2245
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222143
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5212.0192901
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5775268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.17825.24482
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.82215388
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.1551511
X-RAY DIFFRACTIONr_chiral_restr0.10.2332
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021540
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2170.21035
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21445
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2145
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.243
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1190.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0691.51380
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.82222155
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2023860
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5944.5746
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.248 59
Rwork0.223 1198

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