- PDB-5fzl: Crystal structure of the catalytic domain of human JARID1B in com... -
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Basic information
Entry
Database: PDB / ID: 5fzl
Title
Crystal structure of the catalytic domain of human JARID1B in complex with 3D fragment 3-methyl-N-pyridin-4-yl-1,2-oxazole-5-carboxamide (N09954a) (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.: 74 / 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: 41.58 % / Description: NONE
Resolution: 2.55→71.035 Å / SU ML: 0.36 / σ(F): 1.34 / Phase error: 24.43 / Stereochemistry target values: ML Details: LIGAND MODELLED BASED ON PANDDA EVENT MAP. TO BE PUBLISHED.
Rfactor
Num. reflection
% reflection
Rfree
0.2398
1478
4.9 %
Rwork
0.1912
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obs
0.1937
29905
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: 2.55→71.035 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3649
0
67
74
3790
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.009
3894
X-RAY DIFFRACTION
f_angle_d
1.237
5281
X-RAY DIFFRACTION
f_dihedral_angle_d
15.312
1430
X-RAY DIFFRACTION
f_chiral_restr
0.045
556
X-RAY DIFFRACTION
f_plane_restr
0.007
681
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.55-2.6323
0.3691
129
0.3073
2539
X-RAY DIFFRACTION
100
2.6323-2.7264
0.3601
141
0.2859
2523
X-RAY DIFFRACTION
100
2.7264-2.8356
0.3496
132
0.258
2524
X-RAY DIFFRACTION
100
2.8356-2.9646
0.2763
125
0.2388
2550
X-RAY DIFFRACTION
100
2.9646-3.1209
0.2699
142
0.2252
2528
X-RAY DIFFRACTION
100
3.1209-3.3165
0.2568
106
0.222
2577
X-RAY DIFFRACTION
100
3.3165-3.5725
0.2482
126
0.2055
2586
X-RAY DIFFRACTION
100
3.5725-3.932
0.2464
132
0.1834
2580
X-RAY DIFFRACTION
100
3.932-4.5009
0.2154
149
0.1628
2584
X-RAY DIFFRACTION
100
4.5009-5.6703
0.1973
131
0.1548
2651
X-RAY DIFFRACTION
100
5.6703-71.0625
0.2184
165
0.1729
2785
X-RAY DIFFRACTION
100
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