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- PDB-2ng1: N AND GTPASE DOMAINS OF THE SIGNAL SEQUENCE RECOGNITION PROTEIN F... -

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Basic information

Entry
Database: PDB / ID: 2ng1
TitleN AND GTPASE DOMAINS OF THE SIGNAL SEQUENCE RECOGNITION PROTEIN FFH FROM THERMUS AQUATICUS
ComponentsSIGNAL SEQUENCE RECOGNITION PROTEIN FFH
KeywordsSIGNAL RECOGNITION / FFH / SRP / GTPASE / SIGNAL RECOGNITION PARTICLE / GDP
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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / GUANOSINE-5'-DIPHOSPHATE / Signal recognition particle protein
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsFreymann, D.M. / Stroud, R.M. / Walter, P.
Citation
Journal: Nat.Struct.Biol. / Year: 1999
Title: Functional changes in the structure of the SRP GTPase on binding GDP and Mg2+GDP.
Authors: Freymann, D.M. / Keenan, R.J. / Stroud, R.M. / Walter, P.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1998
Title: Crystal Structure of the Signal Sequence Binding Subunit of the Signal Recognition Particle
Authors: Keenan, R.J. / Freymann, D.M. / Walter, P. / Stroud, R.M.
#2: Journal: Nature / Year: 1997
Title: Structure of the Conserved Gtpase Domain of the Signal Recognition Particle
Authors: Freymann, D.M. / Keenan, R.J. / Stroud, R.M. / Walter, P.
History
DepositionSep 11, 1998Processing site: BNL
Revision 1.0Jul 30, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / 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 / _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: SIGNAL SEQUENCE RECOGNITION PROTEIN FFH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8555
Polymers32,1991
Non-polymers6554
Water1,29772
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.425, 54.214, 58.465
Angle α, β, γ (deg.)90.00, 119.62, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein SIGNAL SEQUENCE RECOGNITION PROTEIN FFH / FFH


Mass: 32199.199 Da / Num. of mol.: 1 / Fragment: NG GTPASE FRAGMENT / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Gene: FFH / Plasmid: PET3C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSE / References: UniProt: O07347
#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-DIO / 1,4-DIETHYLENE DIOXIDE / 1,4-Dioxane


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.36 Å3/Da / Density % sol: 47.91 %
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlprotein1drop
22 mMGDP1drop
335 %(v/v)dioxane1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Dec 12, 1996 / Details: YALE MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.02→20 Å / Num. obs: 18481 / % possible obs: 93 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 12.9
Reflection shellResolution: 2.02→2.09 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.284 / Mean I/σ(I) obs: 3.6 / Rsym value: 0.284 / % possible all: 93
Reflection shell
*PLUS
% possible obs: 92.8 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FFH

1ffh


Resolution: 2.02→20 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
Details: A BULK SOLVENT CORRECTION WAS APPLIED. THE DATA QUALITY AND COMPLETENESS BEYOND 2.3 A WERE AFFECTED BY A STRONG ICE RING. THE ELECTRON DENSITY MAPS WERE SOMEWHAT NOISIER THAN WOULD BE ...Details: A BULK SOLVENT CORRECTION WAS APPLIED. THE DATA QUALITY AND COMPLETENESS BEYOND 2.3 A WERE AFFECTED BY A STRONG ICE RING. THE ELECTRON DENSITY MAPS WERE SOMEWHAT NOISIER THAN WOULD BE EXPECTED FOR A STRUCTURE AT THIS RESOLUTION. SEVERAL MAIN CHAIN ATOMS OF THE FOLLOWING SURFACE EXPOSED STRETCHES ARE POORLY DEFINED IN THE ELECTRON DENSITY MAP: 1) PHE 2 - GLN 3, 2) GLY 18 - GLU 25, 3) GLN 63 - GLU 66, AND 4) ALA 251 - ARG 252. THEY ARE CHARACTERIZED BY HIGH TEMPERATURE FACTORS AND ARE PROBABLY MOBILE.
RfactorNum. reflection% reflectionSelection details
Rfree0.29 1446 8 %RANDOM
Rwork0.2 ---
obs0.2 18442 85.1 %-
Displacement parametersBiso mean: 41 Å2
Refinement stepCycle: LAST / Resolution: 2.02→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2261 0 42 72 2375
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.42
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.15
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.73
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.02→2.08 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.35 84 7.5 %
Rwork0.31 1040 -
obs--68 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 16898 / Num. reflection Rfree: 1320 / Rfactor Rfree: 0.291
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.15
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.73

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