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- PDB-5pkh: PanDDA analysis group deposition -- Crystal Structure of JMJD2D a... -

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Basic information

Entry
Database: PDB / ID: 5pkh
TitlePanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 102)
ComponentsLysine-specific demethylase 4D
KeywordsOXIDOREDUCTASE / PanDDA / SGC - Diamond I04-1 fragment screening / Jmj domain / epigenetics
Function / homology
Function and homology information


positive regulation of chromatin binding / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / positive regulation of double-strand break repair via nonhomologous end joining / histone H3K9 demethylase activity / histone demethylase activity / pericentric heterochromatin / cellular response to ionizing radiation / double-strand break repair via homologous recombination / regulation of protein phosphorylation ...positive regulation of chromatin binding / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / positive regulation of double-strand break repair via nonhomologous end joining / histone H3K9 demethylase activity / histone demethylase activity / pericentric heterochromatin / cellular response to ionizing radiation / double-strand break repair via homologous recombination / regulation of protein phosphorylation / HDMs demethylate histones / chromatin DNA binding / site of double-strand break / regulation of gene expression / blood microparticle / damaged DNA binding / chromatin remodeling / inflammatory response / chromatin / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Jelly Rolls ...JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / 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
NICKEL (II) ION / N-OXALYLGLYCINE / Lysine-specific demethylase 4D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.19 Å
AuthorsPearce, N.M. / Krojer, T. / Talon, R. / Bradley, A.R. / Fairhead, M. / Sethi, R. / Wright, N. / MacLean, E. / Collins, P. / Brandao-Neto, J. ...Pearce, N.M. / Krojer, T. / Talon, R. / Bradley, A.R. / Fairhead, M. / Sethi, R. / Wright, N. / MacLean, E. / Collins, P. / Brandao-Neto, J. / Douangamath, A. / Renjie, Z. / Dias, A. / Vollmar, M. / Ng, J. / Szykowska, A. / Burgess-Brown, N. / Brennan, P.E. / Cox, O. / Oppermann, U. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / von Delft, F.
CitationJournal: Nat Commun / Year: 2017
Title: A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density.
Authors: Pearce, N.M. / Krojer, T. / Bradley, A.R. / Collins, P. / Nowak, R.P. / Talon, R. / Marsden, B.D. / Kelm, S. / Shi, J. / Deane, C.M. / von Delft, F.
History
DepositionFeb 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / diffrn_source / pdbx_deposit_group / pdbx_unobs_or_zero_occ_atoms
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _diffrn_source.pdbx_synchrotron_site / _pdbx_deposit_group.group_title / _pdbx_deposit_group.group_type
Revision 1.2Oct 4, 2017Group: Structure summary / Category: pdbx_deposit_group / Item: _pdbx_deposit_group.group_title
Revision 1.3Mar 6, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysine-specific demethylase 4D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,13116
Polymers42,0511
Non-polymers1,08015
Water7,945441
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.406, 71.406, 150.416
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-824-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Lysine-specific demethylase 4D / JmjC domain-containing histone demethylation protein 3D / Jumonji domain-containing protein 2D


Mass: 42050.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KDM4D, JHDM3D, JMJD2D / Production host: Escherichia coli (E. coli) / References: UniProt: Q6B0I6

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Non-polymers , 7 types, 456 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-OGA / N-OXALYLGLYCINE / N-Oxalylglycine


Mass: 147.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5NO5 / Comment: inhibitor*YM
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 441 / 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: 2.28 Å3/Da / Density % sol: 46.05 % / Mosaicity: 0.05 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 28% PEG3350 -- 0.1M HEPES pH 7.0 -- 0.25M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.19→29.39 Å / Num. obs: 94066 / % possible obs: 75.3 % / Redundancy: 11.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.021 / Rrim(I) all: 0.074 / Net I/σ(I): 21.2 / Num. measured all: 1115607 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.19-1.212.10.539208110060.6070.4190.6881.516.8
6.52-29.3911.40.062102238970.9950.0190.06541.498.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0131refinement
Aimless0.1.27data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4D6R
Resolution: 1.19→29.39 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.539 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.043 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1722 4647 4.9 %RANDOM
Rwork0.1533 ---
obs0.1542 89384 75.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 72.1 Å2 / Biso mean: 14.866 Å2 / Biso min: 5.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å2-0 Å2-0 Å2
2--0.1 Å2-0 Å2
3----0.2 Å2
Refinement stepCycle: final / Resolution: 1.19→29.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2664 0 60 442 3166
Biso mean--25.38 29.1 -
Num. residues----330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0193035
X-RAY DIFFRACTIONr_bond_other_d0.0020.022760
X-RAY DIFFRACTIONr_angle_refined_deg2.3891.9424136
X-RAY DIFFRACTIONr_angle_other_deg1.16836362
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5835383
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.61423.6150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.315488
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5531518
X-RAY DIFFRACTIONr_chiral_restr0.1390.2412
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0213575
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02780
X-RAY DIFFRACTIONr_mcbond_it1.5391.2041439
X-RAY DIFFRACTIONr_mcbond_other1.5261.21438
X-RAY DIFFRACTIONr_mcangle_it2.2121.8051835
LS refinement shellResolution: 1.19→1.221 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 92 -
Rwork0.29 1605 -
all-1697 -
obs--18.71 %

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