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- PDB-1zu5: Crystal structure of FtsY from Mycoplasma mycoides- space group H32 -

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Basic information

Entry
Database: PDB / ID: 1zu5
TitleCrystal structure of FtsY from Mycoplasma mycoides- space group H32
ComponentsftsY
KeywordsPROTEIN TRANSPORT / GTPase / FtsY / signal recognition particle / SRP / receptor
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 / 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: 2.4 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 / 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ftsY
B: ftsY


Theoretical massNumber of molelcules
Total (without water)72,2692
Polymers72,2692
Non-polymers00
Water2,504139
1
A: ftsY


Theoretical massNumber of molelcules
Total (without water)36,1351
Polymers36,1351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ftsY


Theoretical massNumber of molelcules
Total (without water)36,1351
Polymers36,1351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)148.441, 148.441, 223.925
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein ftsY / SRP receptor FtsY


Mass: 36134.586 Da / Num. of mol.: 2 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 3.32 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Sodium citrate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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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: Mar 3, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2.4→56 Å / Num. all: 35370 / Num. obs: 35370 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.4→2.49 Å / % possible all: 98.9

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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 CODE 1ZU4

1zu4


Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.926 / SU B: 7.755 / SU ML: 0.178 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.318 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24642 1750 4.9 %RANDOM
Rwork0.2097 ---
all0.2115 35370 --
obs0.21156 33620 94.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.61 Å2
Baniso -1Baniso -2Baniso -3
1--0.78 Å2-0.39 Å20 Å2
2---0.78 Å20 Å2
3---1.17 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4890 0 0 139 5029
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224957
X-RAY DIFFRACTIONr_angle_refined_deg1.6741.9716662
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1765616
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.70126.129217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.82215991
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6051514
X-RAY DIFFRACTIONr_chiral_restr0.110.2771
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023574
X-RAY DIFFRACTIONr_nbd_refined0.2270.22322
X-RAY DIFFRACTIONr_nbtor_refined0.3080.23423
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2211
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.240.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.25
X-RAY DIFFRACTIONr_mcbond_it1.3471.53160
X-RAY DIFFRACTIONr_mcangle_it1.82324943
X-RAY DIFFRACTIONr_scbond_it2.53531936
X-RAY DIFFRACTIONr_scangle_it3.9774.51719
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 113 -
Rwork0.299 2276 -
obs--87.25 %

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