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- PDB-3ng1: N AND GTPASE DOMAINS OF THE SIGNAL SEQUENCE RECOGNITION PROTEIN F... -

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Basic information

Entry
Database: PDB / ID: 3ng1
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
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
: / Signal recognition particle protein
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 13, 1998Processing site: BNL
Revision 1.0Jul 30, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry / _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 SEQUENCE RECOGNITION PROTEIN FFH
B: SIGNAL SEQUENCE RECOGNITION PROTEIN FFH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,71614
Polymers64,6012
Non-polymers1,11512
Water3,531196
1
A: SIGNAL SEQUENCE RECOGNITION PROTEIN FFH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8587
Polymers32,3001
Non-polymers5576
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SIGNAL SEQUENCE RECOGNITION PROTEIN FFH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8587
Polymers32,3001
Non-polymers5576
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.310, 99.010, 99.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (1, 0.0017, -0.0006), (0.0006, -0.0071, 1), (0.0017, -1, -0.0071)
Vector: 18.3017, 24.9916, 24.7563)

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Components

#1: Protein SIGNAL SEQUENCE RECOGNITION PROTEIN FFH / FFH


Mass: 32300.371 Da / Num. of mol.: 2 / Fragment: NG GTPASE FRAGMENT
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-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE CADMIUM ION WHICH MEDIATES THE CRYSTAL CONTACT (CD 701) IS COORDINATED BY GLU 11 AND GLU 33 OF ...THE CADMIUM ION WHICH MEDIATES THE CRYSTAL CONTACT (CD 701) IS COORDINATED BY GLU 11 AND GLU 33 OF THE MONOMER IN THIS ENTRY, AND BY GLU 46 AND ASP 50 OF AN NCS RELATED MONOMER. THEREFORE THE SIDECHAINS OF GLU 46 AND ASP 50 IN THIS ENTRY COORDINATE THE CADMIUM ION RELATED BY NON-CRYSTALLOGRAPHIC SYMMETRY.

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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: 2.8 Å3/Da / Density % sol: 56.12 %
Crystal growpH: 6.5 / Details: pH 6.50
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
113 mg/mlprotein1drop
25 mM1dropCdSO4
310 %(w/v)PEG80001reservoir
40.1 Msodium cacodylate1reservoir
50.2 Mmagnesium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Date: Jul 5, 1997 / Details: MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 32541 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 14.9
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.417 / Mean I/σ(I) obs: 3.3 / Rsym value: 0.417 / % possible all: 98
Reflection
*PLUS
% possible obs: 98.6 %
Reflection shell
*PLUS
% possible obs: 98.6 %

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Processing

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

1ffh


Resolution: 2.3→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.
RfactorNum. reflection% reflectionSelection details
Rfree0.225 2319 8 %RANDOM
Rwork0.199 ---
obs0.199 28595 86.9 %-
Displacement parametersBiso mean: 35.4 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2267 0 16 98 2381
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.02
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.56
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
Refine LS restraints NCSNCS model details: CONSTRAINTS
LS refinement shellResolution: 2.3→2.38 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.281 203 8 %
Rwork0.262 2104 -
obs--71.5 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.56

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