- PDB-1n9p: Crystal Structure of the Cytoplasmic Domain of G-protein Activate... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 1n9p
Title
Crystal Structure of the Cytoplasmic Domain of G-protein Activated Inward Rectifier Potassium Channel 1
Components
G protein-activated inward rectifier potassium channel 1
Keywords
METAL TRANSPORT / BETA BARREL / CYTOPLASMIC DOMAIN / G PROTEIN / INWARD RECTIFIER / POTASSIUM CHANNEL
Function / homology
Function and homology information
: / G-protein activated inward rectifier potassium channel activity / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / inward rectifier potassium channel activity / regulation of monoatomic ion transmembrane transport / parallel fiber to Purkinje cell synapse / potassium ion import across plasma membrane / voltage-gated potassium channel complex ...: / G-protein activated inward rectifier potassium channel activity / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / inward rectifier potassium channel activity / regulation of monoatomic ion transmembrane transport / parallel fiber to Purkinje cell synapse / potassium ion import across plasma membrane / voltage-gated potassium channel complex / response to electrical stimulus / T-tubule / presynaptic membrane / external side of plasma membrane / cell surface / plasma membrane Similarity search - Function
The biological assembly is a tetramer generated from the subunit in the asymmetric unit by the operations: x,y,z and -y+1/2,x+1/2,z and -x,-y+1,z and y-1/2,-x+1/2,z.
Resolution: 1.8→1.86 Å / Redundancy: 13.2 % / Mean I/σ(I) obs: 12.9 / Num. unique all: 2293 / Rsym value: 0.174 / % possible all: 96.6
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 30 Å / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
% possible obs: 96.6 % / Rmerge(I) obs: 0.174
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Processing
Software
Name
Classification
DENZO
datareduction
SCALEPACK
datascaling
MLPHARE
phasing
CNS
refinement
Refinement
Method to determine structure: MAD / Resolution: 1.8→10 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber Details: Methionine was replaced by selenomethionine through refinement and anomalous signal of selenium that was based on the experimental value was incorporated. Bijvoet pairs were treated as ...Details: Methionine was replaced by selenomethionine through refinement and anomalous signal of selenium that was based on the experimental value was incorporated. Bijvoet pairs were treated as separate reflections. No test flag was used in the final cycle of refinement.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.253
2237
5 %
RANDOM
Rwork
0.231
-
-
-
all
0.232
44247
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-
obs
0.232
43936
98.8 %
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Solvent computation
Bsol: 56.37 Å2 / ksol: 0.5 e/Å3
Displacement parameters
Biso mean: 21 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.41 Å2
0 Å2
0 Å2
2-
-
0.41 Å2
0 Å2
3-
-
-
-0.82 Å2
Refinement step
Cycle: LAST / Resolution: 1.8→10 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1585
0
0
140
1725
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
X-RAY DIFFRACTION
c_bond_d
0.007
X-RAY DIFFRACTION
c_angle_deg
1.357
X-RAY DIFFRACTION
c_dihedral_angle_d
26.59
X-RAY DIFFRACTION
c_improper_angle_d
1.15
X-RAY DIFFRACTION
c_mcbond_it
1.4
1.5
X-RAY DIFFRACTION
c_mcangle_it
2.4
2
X-RAY DIFFRACTION
c_scbond_it
2.1
2
X-RAY DIFFRACTION
c_scangle_it
3.1
2.5
LS refinement shell
Resolution: 1.8→1.86 Å / Total num. of bins used: 10
Rfactor
Num. reflection
% reflection
Rfree
0.319
215
4.8 %
Rwork
0.258
4054
-
obs
-
5336
95.3 %
Xplor file
Refine-ID
Serial no
Param file
Topol file
X-RAY DIFFRACTION
1
protein.param
protein.top
X-RAY DIFFRACTION
2
water.param
water.top
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 10 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-ID
Type
Dev ideal
X-RAY DIFFRACTION
c_angle_deg
1.36
X-RAY DIFFRACTION
c_dihedral_angle_d
X-RAY DIFFRACTION
c_dihedral_angle_deg
26.59
X-RAY DIFFRACTION
c_improper_angle_d
X-RAY DIFFRACTION
c_improper_angle_deg
1.15
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