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- PDB-5fxv: Crystal structure of JmjC domain of human histone demethylase UTY... -

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Basic information

Entry
Database: PDB / ID: 5fxv
TitleCrystal structure of JmjC domain of human histone demethylase UTY in complex with N05859b
ComponentsHISTONE DEMETHYLASE UTY
KeywordsTRANSFERASE / PANDDA / FRAGMENT SOAKING / X-RAY FRAGMENT SCREENING
Function / homology
Function and homology information


[histone H3]-trimethyl-L-lysine27 demethylase / histone H3K27me2/H3K27me3 demethylase activity / MLL3/4 complex / histone demethylase activity / HDMs demethylate histones / chromatin DNA binding / heart development / regulation of gene expression / RNA polymerase II cis-regulatory region sequence-specific DNA binding / nucleoplasm / metal ion binding
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1370 / Cysteine Rich Protein - #20 / : / : / : / Lysine-specific demethylase 6/UTY, C-terminal helical domain / KDM6, GATA-like / Cysteine Rich Protein / Tetratricopeptide repeat / Tetratricopeptide repeat ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1370 / Cysteine Rich Protein - #20 / : / : / : / Lysine-specific demethylase 6/UTY, C-terminal helical domain / KDM6, GATA-like / Cysteine Rich Protein / Tetratricopeptide repeat / Tetratricopeptide repeat / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Ribbon / Tetratricopeptide-like helical domain superfamily / Jelly Rolls / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
: / 4-CARBOXYPIPERIDINE / Histone demethylase UTY
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsNowak, R. / Krojer, T. / Johansson, C. / Gileadi, C. / Kupinska, K. / Srikannathasan, V. / Oerum, S. / Pearce, N.M. / von Delft, F. / Arrowsmith, C.H. ...Nowak, R. / Krojer, T. / Johansson, C. / Gileadi, C. / Kupinska, K. / Srikannathasan, V. / Oerum, S. / Pearce, N.M. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Oppermann, U.
CitationJournal: To be Published
Title: Crystal Structure of Jmjc Domain of Human Histone Demethylase Uty in Complex with N05859B
Authors: Nowak, R. / Tobias, K. / Johansson, C. / Gileadi, C. / Kupinska, K. / Srikannathasan, V. / Oerum, S. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Oppermann, U. / Brennan, P.
History
DepositionMar 3, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Jan 10, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HISTONE DEMETHYLASE UTY
B: HISTONE DEMETHYLASE UTY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,13218
Polymers110,0132
Non-polymers1,12016
Water13,854769
1
A: HISTONE DEMETHYLASE UTY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,62810
Polymers55,0061
Non-polymers6229
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HISTONE DEMETHYLASE UTY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5048
Polymers55,0061
Non-polymers4987
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.650, 109.910, 117.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein HISTONE DEMETHYLASE UTY / UBIQUITOUSLY-TRANSCRIBED TPR PROTEIN ON THE Y CHROMOSOME / UBIQUITOUSLY-TRANSCRIBED Y CHROMOSOME ...UBIQUITOUSLY-TRANSCRIBED TPR PROTEIN ON THE Y CHROMOSOME / UBIQUITOUSLY-TRANSCRIBED Y CHROMOSOME TETRATRICOPEPTIDE REPEAT PROTEIN


Mass: 55006.402 Da / Num. of mol.: 2 / Fragment: JMJC DOMAIN, RESIDUES 878-1347
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: O14607

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Non-polymers , 5 types, 785 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-MN1 / 4-CARBOXYPIPERIDINE / Isonipecotic acid


Mass: 129.157 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H11NO2 / Comment: agonist*YM
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 769 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.68 % / Description: NONE
Crystal growpH: 7.2 / Details: 0.1M HEPES PH 7.2 -- 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.92008
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92008 Å / Relative weight: 1
ReflectionResolution: 1.91→41.9 Å / Num. obs: 91818 / % possible obs: 99.9 % / Observed criterion σ(I): 1.1 / Redundancy: 6.5 % / Biso Wilson estimate: 32.6 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.9
Reflection shellResolution: 1.91→1.96 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
DIMPLEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZLI

3zli


Resolution: 1.91→41.902 Å / SU ML: 0.27 / σ(F): 1.33 / Phase error: 26.34 / Stereochemistry target values: ML / Details: DISORDERED SIDE CHAINS WERE REMOVED
RfactorNum. reflection% reflection
Rfree0.2399 4542 4.9 %
Rwork0.1986 --
obs0.2007 91725 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.91→41.902 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7018 0 62 769 7849
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087295
X-RAY DIFFRACTIONf_angle_d1.069936
X-RAY DIFFRACTIONf_dihedral_angle_d12.472604
X-RAY DIFFRACTIONf_chiral_restr0.0481098
X-RAY DIFFRACTIONf_plane_restr0.0051274
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.93170.39661610.39062883X-RAY DIFFRACTION100
1.9317-1.95440.38751630.35842847X-RAY DIFFRACTION100
1.9544-1.97830.36691560.33392862X-RAY DIFFRACTION100
1.9783-2.00330.32571560.30732864X-RAY DIFFRACTION100
2.0033-2.02970.27341540.2842876X-RAY DIFFRACTION100
2.0297-2.05750.32321250.2752919X-RAY DIFFRACTION100
2.0575-2.08690.33981540.26682849X-RAY DIFFRACTION100
2.0869-2.1180.29871470.25042892X-RAY DIFFRACTION100
2.118-2.15110.27791510.23542876X-RAY DIFFRACTION100
2.1511-2.18640.30411460.2382902X-RAY DIFFRACTION100
2.1864-2.22410.29521780.22162851X-RAY DIFFRACTION100
2.2241-2.26450.30061560.21772879X-RAY DIFFRACTION100
2.2645-2.30810.24511540.22232876X-RAY DIFFRACTION100
2.3081-2.35520.27231630.2172867X-RAY DIFFRACTION100
2.3552-2.40640.29321600.22142876X-RAY DIFFRACTION100
2.4064-2.46240.29811600.21622882X-RAY DIFFRACTION100
2.4624-2.52390.27641110.20782946X-RAY DIFFRACTION100
2.5239-2.59220.23481370.20672889X-RAY DIFFRACTION100
2.5922-2.66840.26881630.20532890X-RAY DIFFRACTION100
2.6684-2.75450.22741340.19952942X-RAY DIFFRACTION100
2.7545-2.8530.23881580.19262888X-RAY DIFFRACTION100
2.853-2.96720.24921490.19482918X-RAY DIFFRACTION100
2.9672-3.10220.23341630.19692903X-RAY DIFFRACTION100
3.1022-3.26570.23541400.19462909X-RAY DIFFRACTION100
3.2657-3.47020.24621320.20362962X-RAY DIFFRACTION100
3.4702-3.7380.25091520.18312924X-RAY DIFFRACTION100
3.738-4.11380.18381350.17032977X-RAY DIFFRACTION100
4.1138-4.70840.19011680.14912915X-RAY DIFFRACTION99
4.7084-5.92940.19091620.1663009X-RAY DIFFRACTION100
5.9294-41.9120.19631540.1723110X-RAY DIFFRACTION99

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