- PDB-5fzo: Crystal structure of the catalytic domain of human JmjD1C -
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Basic information
Entry
Database: PDB / ID: 5fzo
Title
Crystal structure of the catalytic domain of human JmjD1C
Components
(PROBABLE JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROT EIN ...) x 2
Keywords
OXIDOREDUCTASE / JMJD1C
Function / homology
Function and homology information
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 / nuclear thyroid hormone receptor binding / dioxygenase activity / histone H3K9 demethylase activity / histone deacetylase complex / transcription coregulator activity / chromatin DNA binding / blood coagulation / Factors involved in megakaryocyte development and platelet production / regulation of DNA-templated transcription ...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 / nuclear thyroid hormone receptor binding / dioxygenase activity / histone H3K9 demethylase activity / histone deacetylase complex / transcription coregulator activity / chromatin DNA binding / blood coagulation / Factors involved in megakaryocyte development and platelet production / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding Similarity search - Function
Histone demethylase JHDM2-like / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Jelly Rolls / Sandwich / Mainly Beta Similarity search - Domain/homology
PROBABLE JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROT EIN ... , 2 types, 2 molecules AB
#1: Protein
PROBABLEJMJCDOMAIN-CONTAININGHISTONEDEMETHYLATIONPROTEIN2C / JUMONJI DOMAIN-CONTAINING PROTEIN 1C / THYROID RECEPTOR-INTERACTING PROTEIN 8 / TR-INTERACTING ...JUMONJI DOMAIN-CONTAINING PROTEIN 1C / THYROID RECEPTOR-INTERACTING PROTEIN 8 / TR-INTERACTING PROTEIN 8 / TRIP-8
Mass: 40373.176 Da / Num. of mol.: 1 / Fragment: JUMONJI DOMAIN, UNP RESIDUES 2157-2500 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-CTHF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 References: UniProt: Q15652, 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
#2: Protein
PROBABLEJMJCDOMAIN-CONTAININGHISTONEDEMETHYLATIONPROTEIN2C / JUMONJI DOMAIN-CONTAINING PROTEIN 1C / THYROID RECEPTOR-INTERACTING PROTEIN 8 / TR-INTERACTING ...JUMONJI DOMAIN-CONTAINING PROTEIN 1C / THYROID RECEPTOR-INTERACTING PROTEIN 8 / TR-INTERACTING PROTEIN 8 / TRIP-8
Mass: 40401.184 Da / Num. of mol.: 1 / Fragment: JUMONJI DOMAIN, UNP RESIDUES 2157-2500 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-CTHF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 References: UniProt: Q15652, 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
Resolution: 1.84→55.46 Å / SU ML: 0.26 / σ(F): 1.34 / Phase error: 25.24 / Stereochemistry target values: ML Details: CYSTEINE 2317 IN CHAIN A AND B IS MODIFIED TO SULFENIC ACID (CSD).
Rfactor
Num. reflection
% reflection
Rfree
0.2314
3626
5 %
Rwork
0.1925
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-
obs
0.1945
72668
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: 1.84→55.46 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
5338
0
16
502
5856
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.008
5652
X-RAY DIFFRACTION
f_angle_d
1.145
7697
X-RAY DIFFRACTION
f_dihedral_angle_d
13.435
2042
X-RAY DIFFRACTION
f_chiral_restr
0.05
841
X-RAY DIFFRACTION
f_plane_restr
0.006
994
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.84-1.8642
0.3579
135
0.3247
2618
X-RAY DIFFRACTION
99
1.8642-1.8898
0.3265
125
0.3025
2573
X-RAY DIFFRACTION
96
1.8898-1.9168
0.3814
124
0.293
2608
X-RAY DIFFRACTION
100
1.9168-1.9454
0.3139
127
0.2893
2658
X-RAY DIFFRACTION
99
1.9454-1.9758
0.2882
132
0.2656
2562
X-RAY DIFFRACTION
96
1.9758-2.0082
0.3276
125
0.2698
2623
X-RAY DIFFRACTION
100
2.0082-2.0428
0.2602
133
0.2729
2678
X-RAY DIFFRACTION
99
2.0428-2.08
0.3209
130
0.2641
2555
X-RAY DIFFRACTION
97
2.08-2.12
0.2883
146
0.2586
2611
X-RAY DIFFRACTION
100
2.12-2.1632
0.2993
158
0.2499
2601
X-RAY DIFFRACTION
98
2.1632-2.2103
0.2822
157
0.2446
2616
X-RAY DIFFRACTION
100
2.2103-2.2617
0.2626
121
0.2304
2661
X-RAY DIFFRACTION
98
2.2617-2.3183
0.2689
139
0.2178
2588
X-RAY DIFFRACTION
99
2.3183-2.3809
0.256
155
0.2134
2642
X-RAY DIFFRACTION
99
2.3809-2.451
0.2673
144
0.2085
2629
X-RAY DIFFRACTION
99
2.451-2.5301
0.2564
139
0.2053
2650
X-RAY DIFFRACTION
99
2.5301-2.6205
0.2311
143
0.1915
2668
X-RAY DIFFRACTION
100
2.6205-2.7255
0.2495
154
0.1928
2637
X-RAY DIFFRACTION
99
2.7255-2.8495
0.2341
139
0.1919
2656
X-RAY DIFFRACTION
99
2.8495-2.9997
0.2364
136
0.1856
2703
X-RAY DIFFRACTION
100
2.9997-3.1876
0.2138
144
0.1849
2666
X-RAY DIFFRACTION
100
3.1876-3.4337
0.2547
144
0.1763
2699
X-RAY DIFFRACTION
100
3.4337-3.7792
0.1978
133
0.1578
2745
X-RAY DIFFRACTION
100
3.7792-4.3259
0.199
138
0.1519
2706
X-RAY DIFFRACTION
100
4.3259-5.4494
0.1516
142
0.145
2780
X-RAY DIFFRACTION
100
5.4494-55.4852
0.196
163
0.1792
2909
X-RAY DIFFRACTION
99
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