- PDB-3wht: Crystal structure of ERGIC-53/MCFD2, Calcium-free form -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3wht
Title
Crystal structure of ERGIC-53/MCFD2, Calcium-free form
Components
Multiple coagulation factor deficiency protein 2
Protein ERGIC-53
Keywords
PROTEIN TRANSPORT / Beta-sandwich / EF-hand / Cargo receptor / Calcium binding / ER / ERGIC
Function / homology
Function and homology information
Transport to the Golgi and subsequent modification / positive regulation of organelle organization / negative regulation of protein targeting to mitochondrion / Cargo concentration in the ER / endoplasmic reticulum organization / RHOD GTPase cycle / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / RHOC GTPase cycle / Golgi organization ...Transport to the Golgi and subsequent modification / positive regulation of organelle organization / negative regulation of protein targeting to mitochondrion / Cargo concentration in the ER / endoplasmic reticulum organization / RHOD GTPase cycle / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / RHOC GTPase cycle / Golgi organization / D-mannose binding / endoplasmic reticulum-Golgi intermediate compartment / RHOG GTPase cycle / RHOA GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / endoplasmic reticulum to Golgi vesicle-mediated transport / vesicle-mediated transport / endoplasmic reticulum-Golgi intermediate compartment membrane / sarcomere / ER to Golgi transport vesicle membrane / blood coagulation / unfolded protein binding / protein transport / protein folding / collagen-containing extracellular matrix / Golgi membrane / calcium ion binding / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / extracellular exosome / membrane / metal ion binding Similarity search - Function
Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.201 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.202
1484
5.1 %
RANDOM
Rwork
0.175
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all
0.177
27848
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obs
0.177
27848
96.57 %
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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: 24.173 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.08 Å2
0 Å2
0.01 Å2
2-
-
-0.25 Å2
0 Å2
3-
-
-
-0.73 Å2
Refinement step
Cycle: LAST / Resolution: 1.8→20 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2128
0
15
195
2338
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.012
0.019
2193
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
2019
X-RAY DIFFRACTION
r_angle_refined_deg
1.491
1.932
2968
X-RAY DIFFRACTION
r_angle_other_deg
0.773
3.001
4626
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.438
5
266
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
30.69
24.561
114
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.886
15
343
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
14.976
15
11
X-RAY DIFFRACTION
r_chiral_restr
0.097
0.2
315
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.02
2529
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
544
LS refinement shell
Resolution: 1.8→1.847 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.256
90
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Rwork
0.244
1953
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obs
-
-
91 %
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