- PDB-5fz3: Crystal structure of the catalytic domain of human JARID1B in com... -
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Open data
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Basic information
Entry
Database: PDB / ID: 5fz3
Title
Crystal structure of the catalytic domain of human JARID1B in complex with Maybridge fragment 3,6-Dihydroxybenzonorbornane (N08776b) (ligand modelled based on PANDDA event map)
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.: 182 / 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: 43.3 % / Description: NONE
Resolution: 2.5→71.585 Å / SU ML: 0.29 / σ(F): 1.35 / Phase error: 22.4 / Stereochemistry target values: ML Details: LIGAND MODELLED BASED ON PANDDA EVENT MAP TO BE PUBLISHED.
Rfactor
Num. reflection
% reflection
Rfree
0.2171
1608
4.9 %
Rwork
0.171
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obs
0.1733
32695
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: 2.5→71.585 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3654
0
74
182
3910
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.009
3919
X-RAY DIFFRACTION
f_angle_d
1.136
5324
X-RAY DIFFRACTION
f_dihedral_angle_d
14.547
1444
X-RAY DIFFRACTION
f_chiral_restr
0.046
563
X-RAY DIFFRACTION
f_plane_restr
0.006
693
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.5-2.5807
0.3182
134
0.2405
2774
X-RAY DIFFRACTION
100
2.5807-2.673
0.3076
135
0.2242
2771
X-RAY DIFFRACTION
100
2.673-2.78
0.2841
160
0.2053
2770
X-RAY DIFFRACTION
100
2.78-2.9065
0.2723
153
0.2004
2763
X-RAY DIFFRACTION
100
2.9065-3.0598
0.2859
124
0.1964
2802
X-RAY DIFFRACTION
100
3.0598-3.2515
0.2225
160
0.192
2787
X-RAY DIFFRACTION
100
3.2515-3.5025
0.2387
103
0.184
2847
X-RAY DIFFRACTION
100
3.5025-3.855
0.212
161
0.1669
2807
X-RAY DIFFRACTION
100
3.855-4.4127
0.1811
159
0.143
2827
X-RAY DIFFRACTION
100
4.4127-5.5593
0.169
144
0.1322
2895
X-RAY DIFFRACTION
100
5.5593-71.6143
0.1985
175
0.1672
3044
X-RAY DIFFRACTION
100
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