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- PDB-2ffh: THE SIGNAL SEQUENCE BINDING PROTEIN FFH FROM THERMUS AQUATICUS -

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Basic information

Entry
Database: PDB / ID: 2ffh
TitleTHE SIGNAL SEQUENCE BINDING PROTEIN FFH FROM THERMUS AQUATICUS
ComponentsPROTEIN (FFH)
KeywordsPROTEIN TRANSPORT / FFH / SRP54 / SIGNAL RECOGNITION PARTICLE / GTPASE / M DOMAIN / RNA-BINDING / SIGNAL SEQUENCE-BINDING / HELIX-TURN-HELIX / PROTEIN TARGETING
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
Signal recognition particle, SRP54 subunit, M-domain / 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 subunit, M-domain / 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 / 434 Repressor (Amino-terminal 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 / Orthogonal Bundle / 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 / MIR, MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsKeenan, R.J. / Freymann, D.M. / Walter, P. / Stroud, R.M.
Citation
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.
#1: 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
DepositionJun 29, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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 / 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_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

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Assembly

Deposited unit
A: PROTEIN (FFH)
B: PROTEIN (FFH)
C: PROTEIN (FFH)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,52122
Polymers140,4343
Non-polymers2,08719
Water00
1
A: PROTEIN (FFH)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4707
Polymers46,8111
Non-polymers6586
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PROTEIN (FFH)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3576
Polymers46,8111
Non-polymers5465
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PROTEIN (FFH)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6949
Polymers46,8111
Non-polymers8838
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
A: PROTEIN (FFH)
B: PROTEIN (FFH)
C: PROTEIN (FFH)
hetero molecules

A: PROTEIN (FFH)
B: PROTEIN (FFH)
C: PROTEIN (FFH)
hetero molecules

A: PROTEIN (FFH)
B: PROTEIN (FFH)
C: PROTEIN (FFH)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)427,56366
Polymers421,3039
Non-polymers6,26057
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area32770 Å2
ΔGint-551 kcal/mol
Surface area161060 Å2
MethodPISA
5
A: PROTEIN (FFH)
B: PROTEIN (FFH)
C: PROTEIN (FFH)
hetero molecules

A: PROTEIN (FFH)
B: PROTEIN (FFH)
C: PROTEIN (FFH)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)285,04244
Polymers280,8696
Non-polymers4,17438
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area27280 Å2
ΔGint-410 kcal/mol
Surface area101500 Å2
MethodPISA
6
C: PROTEIN (FFH)
hetero molecules

C: PROTEIN (FFH)
hetero molecules

B: PROTEIN (FFH)
hetero molecules

B: PROTEIN (FFH)
hetero molecules

A: PROTEIN (FFH)
hetero molecules

A: PROTEIN (FFH)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)285,04244
Polymers280,8696
Non-polymers4,17438
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation5_566x-y,-y+1,-z+11
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation6_656-x+1,-x+y,-z+11
Buried area13980 Å2
ΔGint-328 kcal/mol
Surface area115240 Å2
MethodPISA
7


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9740 Å2
ΔGint-168 kcal/mol
Surface area54650 Å2
MethodPISA
8
C: PROTEIN (FFH)
hetero molecules

C: PROTEIN (FFH)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,38918
Polymers93,6232
Non-polymers1,76616
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area4280 Å2
ΔGint-112 kcal/mol
Surface area38630 Å2
MethodPISA
9
B: PROTEIN (FFH)
hetero molecules

A: PROTEIN (FFH)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,82713
Polymers93,6232
Non-polymers1,20411
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area3660 Å2
ΔGint-92 kcal/mol
Surface area39270 Å2
MethodPISA
10
C: PROTEIN (FFH)
hetero molecules

B: PROTEIN (FFH)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,05215
Polymers93,6232
Non-polymers1,42913
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
Buried area2570 Å2
ΔGint-97 kcal/mol
Surface area40820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)195.050, 195.050, 335.720
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
DetailsThe bacterial SRP contains one molecule of Ffh bound to one molecule of SRP RNA.

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Components

#1: Protein PROTEIN (FFH) / FIFTY-FOUR HOMOLOG / P48


Mass: 46811.449 Da / Num. of mol.: 3 / Fragment: RESIDUES 1-425 / Mutation: A48T
Source method: isolated from a genetically manipulated source
Details: THE EXPRESSION INSERT WAS GENERATED BY PCR / Source: (gene. exp.) Thermus aquaticus (bacteria) / 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.: 16 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 4.37 Å3/Da / Density % sol: 65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PROTEIN AT 20 MG/ML IN 5 MM HEPES, PH 7.5. CRYSTALLIZED AT RT BY HANGING DROP VAPOR DIFFUSION USING 1.2 M SODIUM ACETATE, 0.12 M CADMIUM SULFATE, 0.1 M TRIS PH 8.5, 20 MM LITHIUM DODECYL ...Details: PROTEIN AT 20 MG/ML IN 5 MM HEPES, PH 7.5. CRYSTALLIZED AT RT BY HANGING DROP VAPOR DIFFUSION USING 1.2 M SODIUM ACETATE, 0.12 M CADMIUM SULFATE, 0.1 M TRIS PH 8.5, 20 MM LITHIUM DODECYL SULFATE, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
25 mMHEPES1drop
31.2 M1reservoirNaOAc
40.1 MTris-HCl1reservoir
5120 mM1reservoirCdSO4
620 mMlithium dodecyl sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.928
DetectorType: PRINCETON 2K / Detector: CCD / Date: Jul 4, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.928 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. all: 40702 / Num. obs: 36791 / % possible obs: 90.4 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 11.3
Reflection shellResolution: 3.2→3.36 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.1 / Num. unique all: 3914 / % possible all: 79.6
Reflection shell
*PLUS
% possible obs: 79.6 %

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Processing

Software
NameVersionClassification
CCP4model building
RAVEmodel building
CNS0.4refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RAVEphasing
RefinementMethod to determine structure: MIR, MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FFH

1ffh


Resolution: 3.2→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The structure was refined using the maximum likelihood target with individual b-factor refinement and bulk solvent correction.
RfactorNum. reflection% reflectionSelection details
Rfree0.296 1862 5.1 %Random
Rwork0.257 ---
all-40702 --
obs-36791 90.4 %-
Displacement parametersBiso mean: 72.9 Å2
Refinement stepCycle: LAST / Resolution: 3.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9453 0 31 0 9484
Refine LS restraints NCSNCS model details: THROUGHOUT REFINEMENT TIGHT NCS RESTRAINTS WERE APPLIED SEPARATELY TO EACH OF THE THREE DOMAINS OF FFH -- N (RESIDUES 1-86), G (RESIDUES 87-307) AND M (RESIDUES 319-418). DURING ...NCS model details: THROUGHOUT REFINEMENT TIGHT NCS RESTRAINTS WERE APPLIED SEPARATELY TO EACH OF THE THREE DOMAINS OF FFH -- N (RESIDUES 1-86), G (RESIDUES 87-307) AND M (RESIDUES 319-418). DURING THE FINAL STAGES OF REBUILDING AND REFINEMENT, NCS RESTRAINTS WERE RELAXED FOR RESIDUES 271-279 (THE CLOSING LOOP), 295-307 (HINGE) AND 345-356 (C-TERMINAL HALF OF THE FINGER LOOP), WHICH ARE INVOLVED IN EITHER CRYSTALLOGRAPHIC OR NON- CRYSTALLOGRAPHIC PACKING CONTACTS.
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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