MEMBRANE PROTEIN / BETA BARREL / FOSCHOLINE-12 / Structural Genomics / PSI-2 / Protein Structure Initiative / Center for Structures of Membrane Proteins / CSMP / Cell membrane / Cell outer membrane / Ion transport / Membrane / Phage recognition / Porin / Transmembrane / Transport / TRANSPORT PROTEIN
Function / homology
Function and homology information
colicin transmembrane transporter activity / monoatomic ion channel complex / porin activity / pore complex / protein homotrimerization / monoatomic ion transmembrane transport / lipopolysaccharide binding / cell outer membrane / disordered domain specific binding / protein transport ...colicin transmembrane transporter activity / monoatomic ion channel complex / porin activity / pore complex / protein homotrimerization / monoatomic ion transmembrane transport / lipopolysaccharide binding / cell outer membrane / disordered domain specific binding / protein transport / monoatomic ion channel activity / lipid binding / identical protein binding / membrane Similarity search - Function
Porin, gammaproteobacterial / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Porin domain, Gram-negative type / Gram-negative porin / Porin, Gram-negative type / Porin / Porin domain superfamily / Porin / Beta Barrel / Mainly Beta Similarity search - Domain/homology
A: Outer membrane protein F B: Outer membrane protein F C: Outer membrane protein F D: Outer membrane protein F E: Outer membrane protein F F: Outer membrane protein F G: Outer membrane protein F H: Outer membrane protein F I: Outer membrane protein F J: Outer membrane protein F K: Outer membrane protein F L: Outer membrane protein F
Resolution: 3.79→49.57 Å / Cor.coef. Fo:Fc: 0.791 / Cor.coef. Fo:Fc free: 0.749 / SU B: 35.787 / SU ML: 0.499 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.741 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.28794
3787
5.1 %
RANDOM
Rwork
0.28017
-
-
-
obs
0.28056
71179
49.57 %
-
all
-
71179
-
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 78.133 Å2
Baniso -1
Baniso -2
Baniso -3
1-
3.55 Å2
0 Å2
3.39 Å2
2-
-
-3.05 Å2
0 Å2
3-
-
-
0.73 Å2
Refinement step
Cycle: LAST / Resolution: 3.79→49.57 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
31524
0
0
0
31524
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.004
0.022
32160
X-RAY DIFFRACTION
r_angle_refined_deg
0.65
1.931
43504
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.19
5
4060
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
32.007
24.989
1748
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
11.579
15
4796
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
14.737
15
132
X-RAY DIFFRACTION
r_chiral_restr
0.044
0.2
4412
X-RAY DIFFRACTION
r_gen_planes_refined
0.002
0.02
25848
X-RAY DIFFRACTION
r_mcbond_it
0.09
1.5
19848
X-RAY DIFFRACTION
r_mcangle_it
0.185
2
31324
X-RAY DIFFRACTION
r_scbond_it
0.272
3
12312
X-RAY DIFFRACTION
r_scangle_it
0.477
4.5
12180
Refine LS restraints NCS
Dom-ID: 1 / Ens-ID: 1 / Number: 2619 / Refine-ID: X-RAY DIFFRACTION / Rms dev position: 0.01 Å
Auth asym-ID
Type
Weight position
A
tightpositional
0.05
B
tightpositional
0.05
C
tightpositional
0.05
D
tightpositional
0.05
E
tightpositional
0.05
F
tightpositional
0.05
G
tightpositional
0.05
H
tightpositional
0.05
I
tightpositional
0.05
J
tightpositional
0.05
K
tightpositional
0.05
L
tightpositional
0.05
A
tightthermal
0.5
B
tightthermal
0.5
C
tightthermal
0.5
D
tightthermal
0.5
E
tightthermal
0.5
F
tightthermal
0.5
G
tightthermal
0.5
H
tightthermal
0.5
I
tightthermal
0.5
J
tightthermal
0.5
K
tightthermal
0.5
L
tightthermal
0.5
LS refinement shell
Resolution: 3.787→3.885 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.324
272
-
Rwork
0.344
4598
-
obs
-
-
87.46 %
+
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