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- PDB-3kvb: Structure of KIAA1718 Jumonji domain in complex with N-oxalylglycine -

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Basic information

Entry
Database: PDB / ID: 3kvb
TitleStructure of KIAA1718 Jumonji domain in complex with N-oxalylglycine
ComponentsJmjC domain-containing histone demethylation protein 1D
KeywordsH3K4ME3 BINDING PROTEIN / TRANSFERASE / Jumonji domain lysine demethylase / Metal-binding / Iron / Nickel ion
Function / homology
Function and homology information


histone H4K20 demethylase activity / histone H3K9me/H3K9me2 demethylase activity / [histone H3]-dimethyl-L-lysine9 demethylase / histone H3K27me2/H3K27me3 demethylase activity / histone H3K36 demethylase activity / 2-oxoglutarate-dependent dioxygenase activity / midbrain development / histone H3K9 demethylase activity / histone demethylase activity / methylated histone binding ...histone H4K20 demethylase activity / histone H3K9me/H3K9me2 demethylase activity / [histone H3]-dimethyl-L-lysine9 demethylase / histone H3K27me2/H3K27me3 demethylase activity / histone H3K36 demethylase activity / 2-oxoglutarate-dependent dioxygenase activity / midbrain development / histone H3K9 demethylase activity / histone demethylase activity / methylated histone binding / transcription coregulator activity / HDMs demethylate histones / Signaling by BRAF and RAF1 fusions / iron ion binding / regulation of transcription by RNA polymerase II / nucleolus / positive regulation of DNA-templated transcription / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1360 / Jumonji, helical domain / Jumonji helical domain / : / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Zinc finger, PHD-type, conserved site ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1360 / Jumonji, helical domain / Jumonji helical domain / : / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Jelly Rolls / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
NICKEL (II) ION / N-OXALYLGLYCINE / OXYGEN MOLECULE / Lysine-specific demethylase 7A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsHorton, J.R. / Upadhyay, A.K. / Qi, H.H. / Zhang, X. / Shi, Y. / Cheng, X.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Enzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases.
Authors: Horton, J.R. / Upadhyay, A.K. / Qi, H.H. / Zhang, X. / Shi, Y. / Cheng, X.
History
DepositionNov 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
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.ptnr1_label_seq_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: JmjC domain-containing histone demethylation protein 1D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3785
Polymers46,0811
Non-polymers2964
Water68538
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: JmjC domain-containing histone demethylation protein 1D
hetero molecules

A: JmjC domain-containing histone demethylation protein 1D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,75510
Polymers92,1622
Non-polymers5938
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area4290 Å2
ΔGint-55 kcal/mol
Surface area30270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.3, 78.3, 289.1
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein JmjC domain-containing histone demethylation protein 1D


Mass: 46081.043 Da / Num. of mol.: 1 / Fragment: Residues 92-488
Source method: isolated from a genetically manipulated source
Details: GST-fusion / Source: (gene. exp.) Homo sapiens (human) / Gene: JHDM1D, KIAA1718 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus / References: UniProt: Q6ZMT4, Transferases
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#4: Chemical ChemComp-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5NO5 / Comment: inhibitor*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.78 Å3/Da / Density % sol: 55.69 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 17-20% (v/v) polyethylene glycol 5000 MME, 0.2 M CaCl2, and 0.1 M BisTris pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 6, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.69→33.67 Å / Num. obs: 15320 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.4 % / Biso Wilson estimate: 37.7 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 13.3
Reflection shellResolution: 2.69→2.79 Å / Redundancy: 8 % / Rmerge(I) obs: 0.394 / Mean I/σ(I) obs: 2.6 / Num. unique all: 1303 / % possible all: 86.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3KV6

3kv6


Resolution: 2.69→33.67 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 358678.44 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.267 711 4.9 %RANDOM
Rwork0.216 ---
obs-14477 93.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.1141 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 54.9 Å2
Baniso -1Baniso -2Baniso -3
1-10.87 Å20 Å20 Å2
2--10.87 Å20 Å2
3----21.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.35 Å
Luzzati d res low-35 Å
Luzzati sigma a0.4 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.69→33.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2941 0 14 38 2993
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_mcbond_it1.31.5
X-RAY DIFFRACTIONc_mcangle_it2.222
X-RAY DIFFRACTIONc_scbond_it1.982
X-RAY DIFFRACTIONc_scangle_it3.072.5
LS refinement shellResolution: 2.69→2.79 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.279 58 5.1 %
Rwork0.287 1079 -
obs-1079 75.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water.paramwater.top

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