- PDB-5fzb: Crystal structure of the catalytic domain of human JARID1B in com... -
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Basic information
Entry
Database: PDB / ID: 5fzb
Title
Crystal structure of the catalytic domain of human JARID1B in complex with Maybridge fragment 4-Pyridylthiourea (N06275b) (ligand modelled based on PANDDA event map, SGC - Diamond I04-1 fragment screening)
Mass: 55228.324 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.: 178 / 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: 43.28 % / Description: NONE
Resolution: 2.18→96.519 Å / SU ML: 0.3 / σ(F): 1.34 / Phase error: 23.86 / Stereochemistry target values: ML Details: LIGAND MODELLED BASED ON PANDDA EVENT MAP. TO BE PUBLISHED. GLYCINE LINKER IS UNOBSERVED.
Rfactor
Num. reflection
% reflection
Rfree
0.2274
2376
4.8 %
Rwork
0.194
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obs
0.1957
48974
99.98 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement step
Cycle: LAST / Resolution: 2.18→96.519 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3674
0
79
178
3931
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.009
3903
X-RAY DIFFRACTION
f_angle_d
1.129
5282
X-RAY DIFFRACTION
f_dihedral_angle_d
15.14
1442
X-RAY DIFFRACTION
f_chiral_restr
0.048
556
X-RAY DIFFRACTION
f_plane_restr
0.006
684
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.18-2.2245
0.3493
125
0.308
2697
X-RAY DIFFRACTION
100
2.2245-2.2729
0.3495
134
0.2974
2697
X-RAY DIFFRACTION
100
2.2729-2.3258
0.2668
132
0.2645
2697
X-RAY DIFFRACTION
100
2.3258-2.384
0.2976
127
0.2595
2706
X-RAY DIFFRACTION
100
2.384-2.4484
0.2868
149
0.2489
2669
X-RAY DIFFRACTION
100
2.4484-2.5205
0.2793
143
0.2529
2703
X-RAY DIFFRACTION
100
2.5205-2.6018
0.2671
119
0.243
2730
X-RAY DIFFRACTION
100
2.6018-2.6948
0.3184
149
0.2405
2705
X-RAY DIFFRACTION
100
2.6948-2.8027
0.2682
146
0.2251
2708
X-RAY DIFFRACTION
100
2.8027-2.9303
0.2866
147
0.2217
2708
X-RAY DIFFRACTION
100
2.9303-3.0848
0.2841
125
0.2258
2736
X-RAY DIFFRACTION
100
3.0848-3.2781
0.2492
149
0.2188
2740
X-RAY DIFFRACTION
100
3.2781-3.5312
0.24
103
0.2056
2771
X-RAY DIFFRACTION
100
3.5312-3.8866
0.2268
162
0.1816
2749
X-RAY DIFFRACTION
100
3.8866-4.449
0.1888
153
0.1523
2776
X-RAY DIFFRACTION
100
4.449-5.6052
0.1756
142
0.139
2824
X-RAY DIFFRACTION
100
5.6052-96.6136
0.1796
171
0.172
2982
X-RAY DIFFRACTION
100
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