- PDB-5fzk: Crystal structure of the catalytic domain of human JARID1B in com... -
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Basic information
Entry
Database: PDB / ID: 5fzk
Title
Crystal structure of the catalytic domain of human JARID1B in complex with 3D fragment N,3-dimethyl-N-(pyridin-3-ylmethyl)-1,2-oxazole-5- carboxamide (N10051a) (ligand modelled based on PANDDA event map, SGC - Diamond I04-1 fragment screening)
Journal: To be Published Title: Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with 3D Fragment N,3-Dimethyl-N-(Pyridin-3-Ylmethyl)-1,2-Oxazole-5-Carboxamide (N10051A) (Ligand Modelled Based on Pandda ...Title: Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with 3D Fragment N,3-Dimethyl-N-(Pyridin-3-Ylmethyl)-1,2-Oxazole-5-Carboxamide (N10051A) (Ligand Modelled Based on Pandda Event Map, Sgc - Diamond I04-1 Fragment Screening) Authors: Nowak, R. / Krojer, T. / Johansson, C. / Gileadi, C. / Kupinska, K. / Strain-Damerell, C. / Szykowska, A. / Talon, R. / Collins, P. / Burgess-Brown, N.A. / Arrowsmith, C.H. / Bountra, C. / ...Authors: Nowak, R. / Krojer, T. / Johansson, C. / Gileadi, C. / Kupinska, K. / Strain-Damerell, C. / Szykowska, A. / Talon, R. / Collins, P. / Burgess-Brown, N.A. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / von Delft, F. / Brennan, P.E. / Oppermann, U.
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.: 232 / 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: 2.12 Å3/Da / Density % sol: 41.88 % / Description: NONE
Resolution: 2.05→71.025 Å / SU ML: 0.26 / σ(F): 1.34 / Phase error: 24.69 / Stereochemistry target values: ML Details: LIGAND MODELLED BASED ON PANDDA EVENT MAP. TO BE PUBLISHED. GLYCINE LINKER DOES NOT EXIST.
Rfactor
Num. reflection
% reflection
Rfree
0.2382
2776
4.9 %
Rwork
0.2037
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obs
0.2054
57140
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: 2.05→71.025 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3657
0
69
232
3958
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.009
3914
X-RAY DIFFRACTION
f_angle_d
1.161
5311
X-RAY DIFFRACTION
f_dihedral_angle_d
14.696
1442
X-RAY DIFFRACTION
f_chiral_restr
0.048
559
X-RAY DIFFRACTION
f_plane_restr
0.006
685
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.05-2.0854
0.3445
135
0.3169
2681
X-RAY DIFFRACTION
100
2.0854-2.1233
0.3218
151
0.2919
2667
X-RAY DIFFRACTION
100
2.1233-2.1641
0.2652
125
0.2745
2661
X-RAY DIFFRACTION
100
2.1641-2.2083
0.2812
124
0.2616
2693
X-RAY DIFFRACTION
100
2.2083-2.2563
0.3221
132
0.257
2682
X-RAY DIFFRACTION
100
2.2563-2.3088
0.2375
130
0.2377
2663
X-RAY DIFFRACTION
100
2.3088-2.3666
0.2667
135
0.2349
2712
X-RAY DIFFRACTION
100
2.3666-2.4306
0.276
139
0.2359
2661
X-RAY DIFFRACTION
100
2.4306-2.5021
0.2749
145
0.2418
2684
X-RAY DIFFRACTION
100
2.5021-2.5828
0.2525
119
0.2369
2724
X-RAY DIFFRACTION
100
2.5828-2.6752
0.311
147
0.2355
2677
X-RAY DIFFRACTION
100
2.6752-2.7823
0.259
149
0.2266
2700
X-RAY DIFFRACTION
100
2.7823-2.9089
0.2636
144
0.2263
2678
X-RAY DIFFRACTION
100
2.9089-3.0623
0.2824
122
0.2211
2732
X-RAY DIFFRACTION
100
3.0623-3.2541
0.2512
150
0.2214
2721
X-RAY DIFFRACTION
100
3.2541-3.5054
0.2657
106
0.2062
2763
X-RAY DIFFRACTION
100
3.5054-3.8581
0.2256
160
0.186
2735
X-RAY DIFFRACTION
100
3.8581-4.4163
0.1937
152
0.165
2758
X-RAY DIFFRACTION
100
4.4163-5.5638
0.1856
140
0.1567
2816
X-RAY DIFFRACTION
100
5.5638-71.0676
0.2211
171
0.1861
2956
X-RAY DIFFRACTION
100
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