- PDB-5fza: 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: 5fza
Title
Crystal structure of the catalytic domain of human JARID1B in complex with 3D fragment 2-piperidin-4-yloxy-5-(trifluoromethyl)pyridine (N10072a) (ligand modelled based on PANDDA event map)
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.: 283 / 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: 2.11 Å3/Da / Density % sol: 41.72 % / Description: NONE
Resolution: 2.099→29.706 Å / SU ML: 0.23 / σ(F): 1.36 / Phase error: 23.09 / Stereochemistry target values: ML Details: LIGAND MODELLED BASED ON PANDDA EVENT MAP. TO BE PUBLISHED. GLYCINE LINKER IS UNOBSERVED.
Rfactor
Num. reflection
% reflection
Rfree
0.228
2665
5 %
Rwork
0.1927
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obs
0.1945
53085
99.89 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement step
Cycle: LAST / Resolution: 2.099→29.706 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3660
0
77
283
4020
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.008
3948
X-RAY DIFFRACTION
f_angle_d
1.11
5361
X-RAY DIFFRACTION
f_dihedral_angle_d
14.008
1453
X-RAY DIFFRACTION
f_chiral_restr
0.047
562
X-RAY DIFFRACTION
f_plane_restr
0.006
690
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.0989-2.1371
0.2672
106
0.2481
2595
X-RAY DIFFRACTION
98
2.1371-2.1782
0.2787
122
0.2408
2634
X-RAY DIFFRACTION
100
2.1782-2.2226
0.2979
149
0.2453
2582
X-RAY DIFFRACTION
100
2.2226-2.2709
0.2742
128
0.2377
2625
X-RAY DIFFRACTION
100
2.2709-2.3237
0.2764
163
0.2296
2609
X-RAY DIFFRACTION
100
2.3237-2.3818
0.2648
138
0.2323
2594
X-RAY DIFFRACTION
100
2.3818-2.4462
0.274
146
0.2272
2628
X-RAY DIFFRACTION
100
2.4462-2.5181
0.2563
154
0.2285
2602
X-RAY DIFFRACTION
100
2.5181-2.5994
0.2543
129
0.216
2634
X-RAY DIFFRACTION
100
2.5994-2.6922
0.317
142
0.2246
2620
X-RAY DIFFRACTION
100
2.6922-2.7999
0.2586
147
0.2227
2632
X-RAY DIFFRACTION
100
2.7999-2.9273
0.2463
146
0.2106
2649
X-RAY DIFFRACTION
100
2.9273-3.0814
0.2371
155
0.2144
2632
X-RAY DIFFRACTION
100
3.0814-3.2743
0.2387
126
0.2053
2674
X-RAY DIFFRACTION
100
3.2743-3.5267
0.1991
140
0.1925
2671
X-RAY DIFFRACTION
100
3.5267-3.8809
0.2488
129
0.1776
2688
X-RAY DIFFRACTION
100
3.8809-4.4409
0.2022
162
0.1549
2702
X-RAY DIFFRACTION
100
4.4409-5.589
0.1599
140
0.146
2739
X-RAY DIFFRACTION
100
5.589-29.7089
0.2028
143
0.182
2910
X-RAY DIFFRACTION
100
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