- PDB-3n2n: The Crystal Structure of Tumor Endothelial Marker 8 (TEM8) extrac... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3n2n
Title
The Crystal Structure of Tumor Endothelial Marker 8 (TEM8) extracellular domain
Components
Anthrax toxin receptor 1
Keywords
TOXIN RECEPTOR / Rossmann fold / Anthrax
Function / homology
Function and homology information
reproductive process / filopodium membrane / negative regulation of extracellular matrix assembly / blood vessel development / lamellipodium membrane / Uptake and function of anthrax toxins / collagen binding / substrate adhesion-dependent cell spreading / transmembrane signaling receptor activity / actin filament binding ...reproductive process / filopodium membrane / negative regulation of extracellular matrix assembly / blood vessel development / lamellipodium membrane / Uptake and function of anthrax toxins / collagen binding / substrate adhesion-dependent cell spreading / transmembrane signaling receptor activity / actin filament binding / actin cytoskeleton organization / endosome membrane / external side of plasma membrane / cell surface / metal ion binding / plasma membrane Similarity search - Function
Anthrax toxin receptor, C-terminal / Anthrax toxin receptor, extracellular domain / Anthrax receptor C-terminus region / Anthrax receptor extracellular domain / von Willebrand factor, type A domain / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily ...Anthrax toxin receptor, C-terminal / Anthrax toxin receptor, extracellular domain / Anthrax receptor C-terminus region / Anthrax receptor extracellular domain / von Willebrand factor, type A domain / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology
Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.923 / SU B: 2.596 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.22927
4573
5 %
RANDOM
Rwork
0.19249
-
-
-
obs
0.19434
86821
87.9 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 16.504 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.61 Å2
-0.11 Å2
0.43 Å2
2-
-
0.09 Å2
-0.83 Å2
3-
-
-
1.34 Å2
Refinement step
Cycle: LAST / Resolution: 1.8→50 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
9012
0
78
1353
10443
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.006
0.022
9270
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
0.887
1.945
12474
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.982
5
1104
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.371
23.659
492
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.008
15
1596
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
13.645
15
66
X-RAY DIFFRACTION
r_chiral_restr
0.064
0.2
1314
X-RAY DIFFRACTION
r_gen_planes_refined
0.003
0.02
7170
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
0.308
1.5
5532
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
0.625
2
8820
X-RAY DIFFRACTION
r_scbond_it
1.049
3
3738
X-RAY DIFFRACTION
r_scangle_it
1.849
4.5
3654
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 1.7→1.744 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.375
136
-
Rwork
0.371
2792
-
obs
-
-
38.5 %
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