- PDB-3aih: Human OS-9 MRH domain complexed with alpha3,alpha6-Man5 -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3aih
Title
Human OS-9 MRH domain complexed with alpha3,alpha6-Man5
Components
Protein OS-9
Keywords
SUGAR BINDING PROTEIN / Beta barrel / Lectin
Function / homology
Function and homology information
endoplasmic reticulum mannose trimming / negative regulation of retrograde protein transport, ER to cytosol / Hrd1p ubiquitin ligase complex / protein retention in ER lumen / : / endoplasmic reticulum quality control compartment / retrograde protein transport, ER to cytosol / protein targeting / ER Quality Control Compartment (ERQC) / response to endoplasmic reticulum stress ...endoplasmic reticulum mannose trimming / negative regulation of retrograde protein transport, ER to cytosol / Hrd1p ubiquitin ligase complex / protein retention in ER lumen / : / endoplasmic reticulum quality control compartment / retrograde protein transport, ER to cytosol / protein targeting / ER Quality Control Compartment (ERQC) / response to endoplasmic reticulum stress / Hh mutants are degraded by ERAD / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / ABC-family proteins mediated transport / transmembrane transport / ubiquitin-dependent protein catabolic process / carbohydrate binding / protease binding / protein ubiquitination / endoplasmic reticulum lumen / endoplasmic reticulum membrane / endoplasmic reticulum Similarity search - Function
Protein OS9-like domain / Glucosidase II beta subunit-like protein / Cation-dependent Mannose-6-phosphate Receptor; Chain A / Mannose-6-phosphate receptor binding domain / MRH domain profile. / Mannose-6-phosphate receptor binding domain superfamily / Distorted Sandwich / Mainly Beta Similarity search - Domain/homology
Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1 Å / Relative weight: 1
Reflection
Resolution: 2.1→50 Å / Num. all: 17542 / Num. obs: 17480 / % possible obs: 99.7 % / Redundancy: 11.4 % / Biso Wilson estimate: 30.3 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 28.5
Reflection shell
Resolution: 2.1→2.18 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 5.5 / Num. unique all: 1694 / % possible all: 100
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Processing
Software
Name
Version
Classification
HKL-2000
datacollection
SHELXS
phasing
REFMAC
5.5.0102
refinement
DENZO
datareduction
SCALEPACK
datascaling
Refinement
Method to determine structure: SAD / Resolution: 2.1→40 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.911 / SU B: 5.571 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.277
881
5.1 %
RANDOM
Rwork
0.228
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-
-
obs
0.23
16555
99.89 %
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all
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16555
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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: 31.263 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-1.19 Å2
-0.59 Å2
0 Å2
2-
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-1.19 Å2
0 Å2
3-
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1.78 Å2
Refinement step
Cycle: LAST / Resolution: 2.1→40 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1836
0
68
79
1983
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.018
0.021
1939
X-RAY DIFFRACTION
r_angle_refined_deg
1.663
1.968
2626
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.276
5
216
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
31.427
22.981
104
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
18.231
15
310
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
17.291
15
17
X-RAY DIFFRACTION
r_chiral_restr
0.123
0.2
271
X-RAY DIFFRACTION
r_gen_planes_refined
0.008
0.021
1473
X-RAY DIFFRACTION
r_mcbond_it
1.133
1.5
1092
X-RAY DIFFRACTION
r_mcangle_it
2.103
2
1749
X-RAY DIFFRACTION
r_scbond_it
2.774
3
847
X-RAY DIFFRACTION
r_scangle_it
4.405
4.5
877
LS refinement shell
Resolution: 2.1→2.154 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.317
54
-
Rwork
0.267
1205
-
obs
-
-
100 %
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