- PDB-5fz7: Crystal structure of the catalytic domain of human JARID1B in com... -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 5fz7
Title
Crystal structure of the catalytic domain of human JARID1B in complex with Maybridge fragment ethyl 2-amino-4-thiophen-2-ylthiophene-3- carboxylate (N06131b) (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.: 174 / Source method: isolated from a natural source / Formula: H2O
-
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).
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.15 Å3/Da / Density % sol: 42.92 % / Description: NONE
Resolution: 2.3→96.334 Å / SU ML: 0.26 / σ(F): 1.35 / Phase error: 23.03 / 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
0.2255
2043
4.9 %
Rwork
0.1844
-
-
obs
0.1865
41625
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: 2.3→96.334 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3667
0
73
174
3914
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.009
3907
X-RAY DIFFRACTION
f_angle_d
1.104
5304
X-RAY DIFFRACTION
f_dihedral_angle_d
14.091
1439
X-RAY DIFFRACTION
f_chiral_restr
0.047
559
X-RAY DIFFRACTION
f_plane_restr
0.006
696
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.3001-2.3536
0.298
126
0.2423
2601
X-RAY DIFFRACTION
100
2.3536-2.4124
0.2559
142
0.224
2568
X-RAY DIFFRACTION
100
2.4124-2.4777
0.2728
128
0.2267
2596
X-RAY DIFFRACTION
100
2.4777-2.5506
0.2847
129
0.2304
2604
X-RAY DIFFRACTION
100
2.5506-2.6329
0.2829
130
0.2231
2593
X-RAY DIFFRACTION
100
2.6329-2.727
0.3192
147
0.2226
2591
X-RAY DIFFRACTION
100
2.727-2.8362
0.2881
132
0.2247
2608
X-RAY DIFFRACTION
100
2.8362-2.9653
0.2881
142
0.2221
2608
X-RAY DIFFRACTION
100
2.9653-3.1216
0.2545
124
0.2092
2640
X-RAY DIFFRACTION
100
3.1216-3.3172
0.2368
129
0.2124
2627
X-RAY DIFFRACTION
100
3.3172-3.5734
0.2136
120
0.1964
2650
X-RAY DIFFRACTION
100
3.5734-3.933
0.2361
139
0.1753
2655
X-RAY DIFFRACTION
100
3.933-4.5021
0.1801
155
0.1487
2660
X-RAY DIFFRACTION
100
4.5021-5.6721
0.1804
133
0.1395
2723
X-RAY DIFFRACTION
100
5.6721-96.4189
0.199
167
0.1689
2858
X-RAY DIFFRACTION
100
+
About Yorodumi
-
News
-
Feb 9, 2022. New format data for meta-information of EMDB entries
New format data for meta-information of EMDB entries
Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi