- PDB-5fzm: Crystal structure of the catalytic domain of human JARID1B in com... -
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Basic information
Entry
Database: PDB / ID: 5fzm
Title
Crystal structure of the catalytic domain of human JARID1B in complex with 3D fragment 5-(2-fluorophenyl)-1,3-oxazole-4-carboxylic acid (N09989b) (ligand modelled based on PANDDA event map, SGC - Diamond I04-1 fragment screening)
Mass: 55144.180 Da / Num. of mol.: 1 / Fragment: JMJC DOMAIN, RESIDUES, JMJC DOMAIN, RESIDUES 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.: 111 / 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: 2.1 Å3/Da / Density % sol: 41.41 % / Description: NONE
Resolution: 2.49→70.94 Å / SU ML: 0.35 / σ(F): 1.34 / Phase error: 24.26 / Stereochemistry target values: ML Details: LIGAND MODELLED BASED ON PANDDA EVENT MAP. TO BE PUBLISHED. GLYCINE LINKER DOES NOT EXIST. LIGAND MODELLED BASED ON PANDDA EVENT MAP. TO BE PUBLISHED.
Rfactor
Num. reflection
% reflection
Rfree
0.2243
1571
4.9 %
Rwork
0.1828
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obs
0.1848
32086
99.97 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement step
Cycle: LAST / Resolution: 2.49→70.94 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3637
0
75
111
3823
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.009
3888
X-RAY DIFFRACTION
f_angle_d
1.18
5278
X-RAY DIFFRACTION
f_dihedral_angle_d
14.991
1418
X-RAY DIFFRACTION
f_chiral_restr
0.043
558
X-RAY DIFFRACTION
f_plane_restr
0.006
679
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.49-2.5704
0.3428
120
0.3041
2730
X-RAY DIFFRACTION
100
2.5704-2.6623
0.3641
148
0.2833
2716
X-RAY DIFFRACTION
100
2.6623-2.7688
0.3159
144
0.2536
2706
X-RAY DIFFRACTION
100
2.7688-2.8949
0.3333
153
0.241
2724
X-RAY DIFFRACTION
100
2.8949-3.0475
0.2935
124
0.2191
2753
X-RAY DIFFRACTION
100
3.0475-3.2384
0.2284
147
0.2069
2736
X-RAY DIFFRACTION
100
3.2384-3.4885
0.2382
106
0.1916
2775
X-RAY DIFFRACTION
100
3.4885-3.8395
0.2094
162
0.1725
2765
X-RAY DIFFRACTION
100
3.8395-4.395
0.1821
152
0.1461
2777
X-RAY DIFFRACTION
100
4.395-5.5369
0.1815
144
0.1381
2837
X-RAY DIFFRACTION
100
5.5369-70.9688
0.1982
171
0.1668
2996
X-RAY DIFFRACTION
100
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