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- PDB-1ls1: T. aquaticus Ffh NG Domain at 1.1A Resolution -

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Basic information

Entry
Database: PDB / ID: 1ls1
TitleT. aquaticus Ffh NG Domain at 1.1A Resolution
ComponentsSIGNAL RECOGNITION PARTICLE PROTEIN
KeywordsPROTEIN TRANSPORT / Ffh / SRP54 / SRP / GTPase / ultrahigh resolution
Function / homology
Function and homology information


signal recognition particle / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / GTPase activity / GTP binding / ATP hydrolysis activity
Similarity search - Function
SRP54, nucleotide-binding domain / Signal recognition particle protein / SRP/SRP receptor, N-terminal / Signal recognition particle, SRP54 subunit / Signal recognition particle, SRP54 subunit, M-domain / Signal recognition particle, SRP54 subunit, M-domain superfamily / Signal peptide binding domain / SRP54-type proteins GTP-binding domain signature. / Signal recognition particle SRP54, helical bundle / Signal recognition particle SRP54, N-terminal domain superfamily ...SRP54, nucleotide-binding domain / Signal recognition particle protein / SRP/SRP receptor, N-terminal / Signal recognition particle, SRP54 subunit / Signal recognition particle, SRP54 subunit, M-domain / Signal recognition particle, SRP54 subunit, M-domain superfamily / Signal peptide binding domain / 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
OXYGEN MOLECULE / Signal recognition particle protein
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR SUBSTITUTION / Resolution: 1.1 Å
AuthorsRamirez, U.D. / Minasov, G. / Freymann, D.M.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Structural Basis for Mobility in the 1.1 A Crystal Structure of the NG Domain of Thermus aquaticus Ffh
Authors: Ramirez, U.D. / Minasov, G. / Focia, P.J. / Stroud, R.M. / Walter, P. / Kuhn, P. / Freymann, D.M.
History
DepositionMay 16, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: SIGNAL RECOGNITION PARTICLE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4785
Polymers32,3571
Non-polymers1204
Water5,116284
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.734, 53.675, 57.836
Angle α, β, γ (deg.)90.00, 119.92, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-729-

HOH

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Components

#1: Protein SIGNAL RECOGNITION PARTICLE PROTEIN / FFH / FIFTY-FOUR HOMOLOG


Mass: 32357.422 Da / Num. of mol.: 1 / Fragment: NG domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: O07347
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / 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: 40.65 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9
Details: PEGMME550, MGCl2, TAPS, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
133 mg/mlprotein1drop
230 %PEG550 MME1reservoir
3200 mM1reservoirMgCl2
450 mMTAPS1reservoirpH9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 24, 1997
RadiationMonochromator: SSRL BL 9-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.1→50 Å / Num. obs: 102368 / % possible obs: 95.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.27 % / Rmerge(I) obs: 0.037 / Rsym value: 0.037
Reflection shellResolution: 1.1→1.12 Å / Redundancy: 2.96 % / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.324 / % possible all: 90
Reflection
*PLUS
Num. measured all: 694235
Reflection shell
*PLUS
% possible obs: 89.9 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
REFMAC5refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR SUBSTITUTION
Starting model: PDB ENTRY 1ffh

1ffh


Resolution: 1.1→50 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.45 / SU ML: 0.021 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.032 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1685 4856 5 %RANDOM
Rwork0.13547 ---
all0.1371 97286 --
obs0.13713 92430 90.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.404 Å2
Refinement stepCycle: LAST / Resolution: 1.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5073 0 12 311 5396
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0212547
X-RAY DIFFRACTIONr_bond_other_d0.0010.022624
X-RAY DIFFRACTIONr_angle_refined_deg2.0932.0023582
X-RAY DIFFRACTIONr_angle_other_deg1.14636000
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8343399
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.07815510
X-RAY DIFFRACTIONr_chiral_restr0.1820.2395
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022966
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02566
X-RAY DIFFRACTIONr_nbd_refined0.2470.3617
X-RAY DIFFRACTIONr_nbd_other0.1940.32804
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2480.5223
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.4590.56
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.318
X-RAY DIFFRACTIONr_symmetry_vdw_other0.220.355
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.527
X-RAY DIFFRACTIONr_mcbond_it3.4511.51597
X-RAY DIFFRACTIONr_mcangle_it4.6522702
X-RAY DIFFRACTIONr_scbond_it7.1233950
X-RAY DIFFRACTIONr_scangle_it10.3914.5880
X-RAY DIFFRACTIONr_rigid_bond_restr4.06352547
X-RAY DIFFRACTIONr_sphericity_free32.93530323
X-RAY DIFFRACTIONr_sphericity_bonded11.339302490
LS refinement shellResolution: 1.1→1.128 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.214 324
Rwork0.187 5779
Refinement
*PLUS
Lowest resolution: 50 Å / % reflection Rfree: 8 % / Rfactor Rfree: 0.169 / Rfactor Rwork: 0.135
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.024
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.086

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