- PDB-3ri9: Xylanase C from Aspergillus kawachii F131W mutant -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3ri9
Title
Xylanase C from Aspergillus kawachii F131W mutant
Components
Endo-1,4-beta-xylanase 3
Keywords
HYDROLASE / beta-jellyroll / Extracellular
Function / homology
Function and homology information
endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / extracellular region Similarity search - Function
Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 / Glycosyl hydrolases family 11 (GH11) domain / Glycosyl hydrolases family 11 / Glycosyl hydrolases family 11 (GH11) domain profile. / Glycoside hydrolase family 11/12 ...Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 / Glycosyl hydrolases family 11 (GH11) domain / Glycosyl hydrolases family 11 / Glycosyl hydrolases family 11 (GH11) domain profile. / Glycoside hydrolase family 11/12 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta Similarity search - Domain/homology
Resolution: 2→29.98 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.96 / SU B: 3.466 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.21161
783
5 %
RANDOM
Rwork
0.16381
-
-
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all
0.16602
14897
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-
obs
0.16602
14897
100 %
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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: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 38.902 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.09 Å2
0 Å2
0 Å2
2-
-
0.09 Å2
0 Å2
3-
-
-
-0.18 Å2
Refine analyze
Free
Obs
Luzzati coordinate error
0.135 Å
0.134 Å
Refinement step
Cycle: LAST / Resolution: 2→29.98 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1397
0
0
69
1466
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.025
0.021
1439
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
2.07
1.886
1972
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.733
5
181
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
33.834
24.507
71
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.568
15
179
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
6.304
15
3
X-RAY DIFFRACTION
r_chiral_restr
0.165
0.2
207
X-RAY DIFFRACTION
r_gen_planes_refined
0.012
0.02
1155
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
1.485
1.5
893
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
2.622
2
1431
X-RAY DIFFRACTION
r_scbond_it
3.362
3
546
X-RAY DIFFRACTION
r_scangle_it
5.039
4.5
541
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2→2.052 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.324
54
-
Rwork
0.235
1065
-
obs
-
-
100 %
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