- PDB-5fz9: Crystal structure of the catalytic domain of human JARID1B in com... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 5fz9
Title
Crystal structure of the catalytic domain of human JARID1B in complex with Maybridge fragment thieno(3,2-b)thiophene-5-carboxylic acid (N06263b) (ligand modelled based on PANDDA event map, SGC - Diamond I04-1 fragment screening)
Mass: 55214.297 Da / Num. of mol.: 1 / Fragment: JMJC DOMAIN, UNP 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.: 230 / 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: 2.18 Å3/Da / Density % sol: 43.62 % / Description: NONE
Resolution: 2.06→96.729 Å / SU ML: 0.27 / σ(F): 1.34 / Phase error: 24.47 / Stereochemistry target values: ML Details: LIGAND MODELLED BASED ON PANDDA EVENT MAP. TO BE PUBLISHED. GLYCINE LINKER IS UNOBSERVED
Rfactor
Num. reflection
% reflection
Rfree
0.2278
2828
4.9 %
Rwork
0.1951
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obs
0.1967
58182
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: 2.06→96.729 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3666
0
89
230
3985
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.009
4069
X-RAY DIFFRACTION
f_angle_d
1.106
5540
X-RAY DIFFRACTION
f_dihedral_angle_d
14.494
1527
X-RAY DIFFRACTION
f_chiral_restr
0.052
576
X-RAY DIFFRACTION
f_plane_restr
0.005
753
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.06-2.0955
0.3852
143
0.3158
2682
X-RAY DIFFRACTION
100
2.0955-2.1336
0.3232
141
0.2991
2749
X-RAY DIFFRACTION
100
2.1336-2.1747
0.3278
135
0.2869
2724
X-RAY DIFFRACTION
100
2.1747-2.2191
0.2713
136
0.2662
2713
X-RAY DIFFRACTION
100
2.2191-2.2673
0.3466
131
0.2607
2742
X-RAY DIFFRACTION
100
2.2673-2.3201
0.2898
134
0.2437
2731
X-RAY DIFFRACTION
100
2.3201-2.3781
0.2704
132
0.2381
2733
X-RAY DIFFRACTION
100
2.3781-2.4424
0.2645
141
0.2371
2743
X-RAY DIFFRACTION
100
2.4424-2.5143
0.2774
142
0.232
2731
X-RAY DIFFRACTION
100
2.5143-2.5954
0.2544
129
0.2276
2745
X-RAY DIFFRACTION
100
2.5954-2.6882
0.2762
146
0.2289
2732
X-RAY DIFFRACTION
100
2.6882-2.7959
0.2881
145
0.2196
2749
X-RAY DIFFRACTION
100
2.7959-2.9231
0.2589
156
0.2172
2762
X-RAY DIFFRACTION
100
2.9231-3.0772
0.2799
127
0.2136
2754
X-RAY DIFFRACTION
100
3.0772-3.27
0.2261
152
0.2101
2776
X-RAY DIFFRACTION
100
3.27-3.5225
0.2439
103
0.1988
2816
X-RAY DIFFRACTION
100
3.5225-3.877
0.2192
161
0.1832
2789
X-RAY DIFFRACTION
100
3.877-4.438
0.1716
157
0.153
2798
X-RAY DIFFRACTION
100
4.438-5.5914
0.1797
144
0.1434
2863
X-RAY DIFFRACTION
100
5.5914-96.8353
0.1962
173
0.1748
3022
X-RAY DIFFRACTION
100
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