- PDB-5fz6: Crystal structure of the catalytic domain of human JARID1B in com... -
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Basic information
Entry
Database: PDB / ID: 5fz6
Title
Crystal structure of the catalytic domain of human JARID1B in complex with Maybridge fragment N05859b (ligand modelled based on PANDDA event map, SGC - Diamond I04-1 fragment screening)
Mass: 55214.297 Da / Num. of mol.: 1 / Fragment: JMJC DOMAIN, RESIDUES 26-101,374-770 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFB-LIC-BSE / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) References: UniProt: Q9UGL1, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor
Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O
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Details
Sequence details
RESIDUES S AND M COME FROM THE EXPRESSION VECTOR. RESIDUES 102-373 WERE DELETED FROM THE ORIGINAL ...RESIDUES S AND M COME FROM THE EXPRESSION VECTOR. RESIDUES 102-373 WERE DELETED FROM THE ORIGINAL SEQUENCE Q9UGL1. DELETED RESIDUES WERE LINKED WITH 4 GLYCINE LINKER (GGGG).
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.17 Å3/Da / Density % sol: 43.38 % / Description: NONE
Resolution: 2.33→96.566 Å / SU ML: 0.26 / σ(F): 1.34 / Phase error: 21.88 / Stereochemistry target values: ML Details: LIGAND MODELLED BASED ON PANDDA EVENT MAP. TO BE PUBLISHED.
Rfactor
Num. reflection
% reflection
Rfree
0.2186
1982
4.9 %
Rwork
0.1786
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obs
0.1806
40344
99.99 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement step
Cycle: LAST / Resolution: 2.33→96.566 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3673
0
85
197
3955
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.009
3971
X-RAY DIFFRACTION
f_angle_d
1.138
5389
X-RAY DIFFRACTION
f_dihedral_angle_d
13.989
1476
X-RAY DIFFRACTION
f_chiral_restr
0.049
563
X-RAY DIFFRACTION
f_plane_restr
0.006
696
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.33-2.3883
0.261
132
0.2272
2705
X-RAY DIFFRACTION
100
2.3883-2.4529
0.2664
143
0.2254
2674
X-RAY DIFFRACTION
100
2.4529-2.5251
0.294
146
0.2222
2679
X-RAY DIFFRACTION
100
2.5251-2.6066
0.2354
119
0.2158
2736
X-RAY DIFFRACTION
100
2.6066-2.6997
0.3013
148
0.217
2666
X-RAY DIFFRACTION
100
2.6997-2.8078
0.2377
148
0.2053
2697
X-RAY DIFFRACTION
100
2.8078-2.9356
0.2584
144
0.2045
2691
X-RAY DIFFRACTION
100
2.9356-3.0904
0.2661
122
0.2048
2741
X-RAY DIFFRACTION
100
3.0904-3.2841
0.2204
151
0.2041
2718
X-RAY DIFFRACTION
100
3.2841-3.5376
0.2607
106
0.1966
2768
X-RAY DIFFRACTION
100
3.5376-3.8936
0.2161
158
0.1761
2744
X-RAY DIFFRACTION
100
3.8936-4.4571
0.1878
155
0.1474
2761
X-RAY DIFFRACTION
100
4.4571-5.6154
0.1748
139
0.1336
2814
X-RAY DIFFRACTION
100
5.6154-96.6494
0.1915
171
0.1641
2968
X-RAY DIFFRACTION
100
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