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- PDB-3kv6: Structure of KIAA1718, human Jumonji demethylase, in complex with... -

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Basic information

Entry
Database: PDB / ID: 3kv6
TitleStructure of KIAA1718, human Jumonji demethylase, in complex with alpha-ketoglutarate
ComponentsJmjC domain-containing histone demethylation protein 1D
KeywordsH3K4ME3 BINDING PROTEIN / TRANSFERASE / Epigenetics / Histone Code / Jumonji lysine demethylase / Metal-binding / Zinc-finger
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 / transcription coregulator activity ...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 / transcription coregulator activity / HDMs demethylate histones / Signaling by BRAF and RAF1 fusions / chromatin remodeling / iron ion binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / nucleolus / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1360 / Jumonji, helical domain / Jumonji helical domain / : / Zinc/RING finger domain, C3HC4 (zinc finger) / Cupin / JmjC domain, hydroxylase / Herpes Virus-1 / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1360 / Jumonji, helical domain / Jumonji helical domain / : / Zinc/RING finger domain, C3HC4 (zinc finger) / Cupin / JmjC domain, hydroxylase / Herpes Virus-1 / 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. / Zinc finger PHD-type profile. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / 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 / 2-Layer Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / : / OXYGEN MOLECULE / Lysine-specific demethylase 7A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 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: Non-polymer description / 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_asym_id / _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_asym_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_asym_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_asym_id / _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_asym_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)111,36512
Polymers110,6352
Non-polymers73010
Water2,972165
1
A: JmjC domain-containing histone demethylation protein 1D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6826
Polymers55,3181
Non-polymers3655
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: JmjC domain-containing histone demethylation protein 1D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6826
Polymers55,3181
Non-polymers3655
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: JmjC domain-containing histone demethylation protein 1D
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)111,36512
Polymers110,6352
Non-polymers73010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_665x+1,y+1,z1
Buried area2790 Å2
ΔGint-37 kcal/mol
Surface area41620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.400, 125.200, 206.000
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 AD

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


Mass: 55317.512 Da / Num. of mol.: 2 / Fragment: UNP Residues 1-488
Source method: isolated from a genetically manipulated source
Details: GST-fusion / Source: (gene. exp.) Homo sapiens (human) / Gene: JHDM1D, KIAA1718 / Plasmid: pXC720 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus / References: UniProt: Q6ZMT4, Transferases

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Non-polymers , 5 types, 175 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#5: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 3.69 Å3/Da / Density % sol: 66.71 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
Crystal growpH: 6
Details: 5-10% (v/v) polyethylene glycol 3350, 0.2 M KSCN, and 0.1 M BisTris pH 6.0, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 14, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.89→34.54 Å / Num. obs: 70224 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Biso Wilson estimate: 67 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 16.5
Reflection shellResolution: 2.89→2.99 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 4 / % possible all: 95.6

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2YU2 AND 1WEP

2yu2

1wep


Resolution: 2.89→34.54 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 132891.34 / 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
Rfree0.253 3289 5 %RANDOM
Rwork0.215 ---
obs0.215 66070 93.3 %-
Solvent computationSolvent model: BULK SOLVENT MODELING / Bsol: 12.12 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 34.7 Å2
Baniso -1Baniso -2Baniso -3
1-2.14 Å20 Å20 Å2
2---5.66 Å20 Å2
3---3.52 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.36 Å
Luzzati d res low-35 Å
Luzzati sigma a0.42 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.89→34.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7143 0 30 165 7338
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.031.5
X-RAY DIFFRACTIONc_mcangle_it3.172
X-RAY DIFFRACTIONc_scbond_it1.42
X-RAY DIFFRACTIONc_scangle_it2.22.5
LS refinement shellResolution: 2.89→2.99 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.371 260 4.4 %
Rwork0.329 5603 -
obs--82.7 %
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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