- PDB-3dm5: Structures of SRP54 and SRP19, the two proteins assembling the ri... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3dm5
Title
Structures of SRP54 and SRP19, the two proteins assembling the ribonucleic core of the Signal Recognition Particle from the archaeon Pyrococcus furiosus.
Components
Signal recognition 54 kDa protein
Keywords
RNA BINDING PROTEIN / Transport protein / protein-RNA / Signal Recognition Particle / SRP-GTPase / Protein Targeting / Cytoplasm / GTP-binding / Nucleotide-binding / Ribonucleoprotein / RNA-binding
Function / homology
Function and homology information
signal recognition particle / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / GTPase activity / GTP binding Similarity search - Function
Resolution: 2.51→2.56 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.763 / Mean I/σ(I) obs: 1.7 / Num. unique all: 3675 / Rsym value: 0.763 / % possible all: 98.4
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Processing
Software
Name
Version
Classification
PHENIX
(phenix.refine)
refinement
ELVES
refinement
HKL-2000
datareduction
SCALEPACK
datascaling
PHENIX
phasing
Refinement
Method to determine structure: SAD / Resolution: 2.51→64.74 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.44 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.259
2000
3.8 %
4% OF RANDOMLY SELECTED REFLECTIONS
Rwork
0.222
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-
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obs
0.223
52652
99.5 %
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Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.718 Å2 / ksol: 0.381 e/Å3
Displacement parameters
Biso mean: 40 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-3.8667 Å2
0 Å2
0 Å2
2-
-
-3.8667 Å2
0 Å2
3-
-
-
7.7333 Å2
Refinement step
Cycle: LAST / Resolution: 2.51→64.74 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
6388
0
119
142
6649
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.008
6580
X-RAY DIFFRACTION
f_angle_d
1.168
8874
X-RAY DIFFRACTION
f_dihedral_angle_d
18.932
2478
X-RAY DIFFRACTION
f_chiral_restr
0.07
1024
X-RAY DIFFRACTION
f_plane_restr
0.006
1120
LS refinement shell
Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Num. reflection obs
% reflection obs (%)
2.51-2.57
0.3625
139
0.3102
3517
3517
98
2.57-2.64
0.3107
140
0.2946
3551
99
2.64-2.72
0.3168
141
0.2866
3556
99
4.19-4.8
0.1971
144
0.1533
3662
100
4.8-6.04
0.2238
147
0.1938
3711
100
6.04-64.76
0.2418
152
0.2192
3855
98
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