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- PDB-3ptr: PHF2 Jumonji domain -

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Basic information

Entry
Database: PDB / ID: 3ptr
TitlePHF2 Jumonji domain
ComponentsPHD finger protein 2
KeywordsPROTEIN BINDING / alpha-ketoglutarate-Fe2+ dependent dioxygenases / Histone tail BINDING PROTEIN
Function / homology
Function and homology information


histone H4K20 demethylase activity / negative regulation of rDNA heterochromatin formation / protein demethylation / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / histone H3K9 demethylase activity / transcription initiation-coupled chromatin remodeling / methylated histone binding / liver development / transcription coregulator activity / HDMs demethylate histones ...histone H4K20 demethylase activity / negative regulation of rDNA heterochromatin formation / protein demethylation / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / histone H3K9 demethylase activity / transcription initiation-coupled chromatin remodeling / methylated histone binding / liver development / transcription coregulator activity / HDMs demethylate histones / kinetochore / transcription coactivator activity / iron ion binding / nucleolus / regulation of transcription by RNA polymerase II / 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 / PHD-finger ...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
Lysine-specific demethylase PHF2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.954 Å
AuthorsHorton, J.R. / Upadhyay, A.K. / Hashimoto, H. / Zhang, X. / Cheng, X.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Structural basis for human PHF2 Jumonji domain interaction with metal ions.
Authors: Horton, J.R. / Upadhyay, A.K. / Hashimoto, H. / Zhang, X. / Cheng, X.
History
DepositionDec 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 29, 2012Group: Database references
Revision 1.3Sep 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
B: PHD finger protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,89520
Polymers44,7151
Non-polymers1,17919
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.737, 66.512, 104.567
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PHD finger protein 2 / / GRC5


Mass: 44715.215 Da / Num. of mol.: 1 / Fragment: Jumonji domain (unp residues 60-451)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHF2, KIAA0662 / Plasmid: pXC870 / Production host: Escherichia coli (E. coli) / References: UniProt: O75151
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.56 Å3/Da / Density % sol: 51.88 %
Crystal growMethod: vapor diffusion / pH: 6
Details: 18-30% polyethylene glycol 3350 and 100 mM NaCitrate, pH 5.2-6.0, VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 26, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→34.85 Å / Num. obs: 33743 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 22.55 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 18.8
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.539 / Mean I/σ(I) obs: 3 / Num. unique all: 3254 / % possible all: 97.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3KV4

3kv4


Resolution: 1.954→34.85 Å / SU ML: 0.26 / σ(F): 0.03 / Phase error: 22.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2293 1626 5.13 %
Rwork0.1801 --
obs0.1825 31679 93.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.083 Å2 / ksol: 0.345 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.304 Å2-0 Å20 Å2
2---10.0404 Å2-0 Å2
3---16.3444 Å2
Refinement stepCycle: LAST / Resolution: 1.954→34.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2887 0 76 247 3210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063048
X-RAY DIFFRACTIONf_angle_d0.9854107
X-RAY DIFFRACTIONf_dihedral_angle_d12.9021107
X-RAY DIFFRACTIONf_chiral_restr0.072445
X-RAY DIFFRACTIONf_plane_restr0.004520
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9535-2.02330.25941430.21222601X-RAY DIFFRACTION82
2.0233-2.10430.28391480.20062720X-RAY DIFFRACTION86
2.1043-2.20010.26321600.18952860X-RAY DIFFRACTION90
2.2001-2.31610.211670.18172930X-RAY DIFFRACTION93
2.3161-2.46110.22161610.17943009X-RAY DIFFRACTION94
2.4611-2.65110.23461670.19213050X-RAY DIFFRACTION96
2.6511-2.91780.2351690.18793132X-RAY DIFFRACTION97
2.9178-3.33970.22571710.17763186X-RAY DIFFRACTION98
3.3397-4.20650.18831720.16263228X-RAY DIFFRACTION99
4.2065-34.85740.23441680.17113337X-RAY DIFFRACTION97

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