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- PDB-3kva: Structure of KIAA1718 Jumonji domain in complex with alpha-ketogl... -

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Basic information

Entry
Database: PDB / ID: 3kva
TitleStructure of KIAA1718 Jumonji domain in complex with alpha-ketoglutarate
ComponentsJmjC domain-containing histone demethylation protein 1D
KeywordsH3K4ME3 BINDING PROTEIN / TRANSFERASE / Jumonji domain 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 / : / 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
2-OXOGLUTARIC ACID / : / OXYGEN MOLECULE / Lysine-specific demethylase 7A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 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_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)46,3715
Polymers46,0811
Non-polymers2904
Water90150
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)92,74210
Polymers92,1622
Non-polymers5808
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area4040 Å2
ΔGint-59 kcal/mol
Surface area30720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.1, 78.1, 290.8
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: UNP 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-FE2 / FE (II) ION


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


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#4: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 55.72 %
Description: The Structure Factor File contains Friedel pairs
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-ID / Wavelength: 1.27046 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 20, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.27046 Å / Relative weight: 1
ReflectionResolution: 2.79→34.4 Å / Num. obs: 26944 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 41.5 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 15.5
Reflection shellResolution: 2.79→2.89 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 4.1 / Num. unique all: 1360 / % possible all: 99.3

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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: 3KV6

3kv6


Resolution: 2.79→34.4 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 555080.86 / 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
Rfree0.269 1112 4.7 %RANDOM
Rwork0.203 ---
obs-23589 95.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.4081 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 47.8 Å2
Baniso -1Baniso -2Baniso -3
1-7.56 Å20 Å20 Å2
2--7.56 Å20 Å2
3----15.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.33 Å
Luzzati d res low-35 Å
Luzzati sigma a0.35 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.79→34.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2924 0 14 50 2988
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_mcbond_it0.831.5
X-RAY DIFFRACTIONc_mcangle_it1.472
X-RAY DIFFRACTIONc_scbond_it1.292
X-RAY DIFFRACTIONc_scangle_it2.112.5
LS refinement shellResolution: 2.79→2.89 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.37 107 4.9 %
Rwork0.287 --
obs-2084 89.3 %
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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