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- PDB-1zu4: Crystal structure of FtsY from Mycoplasma mycoides- space group P21212 -

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Basic information

Entry
Database: PDB / ID: 1zu4
TitleCrystal structure of FtsY from Mycoplasma mycoides- space group P21212
ComponentsftsY
KeywordsPROTEIN TRANSPORT / GTPase / FtsY / signal recognition particle / SRP / receptor
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 / plasma membrane / cytoplasm
Similarity search - Function
SRP54, nucleotide-binding domain / Signal-recognition particle receptor FtsY / SRP/SRP receptor, N-terminal / 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 ...SRP54, nucleotide-binding domain / Signal-recognition particle receptor FtsY / SRP/SRP receptor, N-terminal / 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
: / Signal recognition particle receptor FtsY
Similarity search - Component
Biological speciesMycoplasma mycoides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsGariani, T. / Samuelsson, T. / Sauer-Eriksson, A.E.
CitationJournal: J.Struct.Biol. / Year: 2006
Title: Conformational variability of the GTPase domain of the signal recognition particle receptor FtsY
Authors: Gariani, T. / Samuelsson, T. / Sauer-Eriksson, A.E.
History
DepositionMay 30, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: 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 / diffrn_source / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _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: ftsY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2312
Polymers36,1351
Non-polymers961
Water4,540252
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.735, 101.129, 42.533
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1253-

HOH

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Components

#1: Protein ftsY / SRP receptor FtsY


Mass: 36134.586 Da / Num. of mol.: 1 / Fragment: NG domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma mycoides (bacteria) / Plasmid: pet9d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 1929401, UniProt: Q6MTB9*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.07 Å3/Da / Density % sol: 40.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Ammonium sulfate, potassium tartrate, Magnesium Chloride, sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.91 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 19, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.9→56.8 Å / Num. all: 22061 / Num. obs: 22061 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.069
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.321 / % possible all: 79.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FTS

1fts


Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.904 / SU B: 5.601 / SU ML: 0.157 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.248 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26429 2062 10 %RANDOM
Rwork0.20728 ---
all0.213 20702 --
obs0.21302 18640 92.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.713 Å2
Baniso -1Baniso -2Baniso -3
1--1.36 Å20 Å20 Å2
2---0.87 Å20 Å2
3---2.23 Å2
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2404 0 5 252 2661
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222438
X-RAY DIFFRACTIONr_angle_refined_deg1.6241.9773275
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5415303
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.97426.321106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.5615489
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.332157
X-RAY DIFFRACTIONr_chiral_restr0.1060.2380
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021747
X-RAY DIFFRACTIONr_nbd_refined0.2230.21169
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21732
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2210
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2460.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4560.222
X-RAY DIFFRACTIONr_mcbond_it1.4271.51553
X-RAY DIFFRACTIONr_mcangle_it1.84322432
X-RAY DIFFRACTIONr_scbond_it3.0333969
X-RAY DIFFRACTIONr_scangle_it4.5544.5843
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 145 -
Rwork0.284 1323 -
obs--91.64 %

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