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- PDB-2wwu: Crystal structure of the catalytic domain of PHD finger protein 8 -

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Basic information

Entry
Database: PDB / ID: 2wwu
TitleCrystal structure of the catalytic domain of PHD finger protein 8
ComponentsPHD FINGER PROTEIN 8
KeywordsMETAL BINDING PROTEIN / JMJC DOMAIN / EPIGENETICS / METAL-BINDING PROTEIN / HISTONE DEMETHYLASE
Function / homology
Function and homology information


histone H4K20 demethylase activity / histone H3K36me/H3K36me2 demethylase activity / [histone H3]-dimethyl-L-lysine36 demethylase / histone H3K9me/H3K9me2 demethylase activity / [histone H3]-dimethyl-L-lysine9 demethylase / histone H3K27me2/H3K27me3 demethylase activity / negative regulation of rDNA heterochromatin formation / histone H3K36 demethylase activity / 2-oxoglutarate-dependent dioxygenase activity / positive regulation of transcription by RNA polymerase I ...histone H4K20 demethylase activity / histone H3K36me/H3K36me2 demethylase activity / [histone H3]-dimethyl-L-lysine36 demethylase / histone H3K9me/H3K9me2 demethylase activity / [histone H3]-dimethyl-L-lysine9 demethylase / histone H3K27me2/H3K27me3 demethylase activity / negative regulation of rDNA heterochromatin formation / histone H3K36 demethylase activity / 2-oxoglutarate-dependent dioxygenase activity / positive regulation of transcription by RNA polymerase I / histone H3K9 demethylase activity / histone demethylase activity / methylated histone binding / Condensation of Prophase Chromosomes / transcription coregulator activity / HDMs demethylate histones / brain development / G1/S transition of mitotic cell cycle / nuclear membrane / iron ion binding / chromatin binding / nucleolus / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive 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 / Jelly Rolls / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / beta-D-glucopyranose / NICKEL (II) ION / Histone lysine demethylase PHF8
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsYue, W.W. / Hozjan, V. / Cooper, C. / Tumber, A. / Krojer, T. / Muniz, J. / Allerston, C. / Salah, E. / McDonough, M.A. / von Delft, F. ...Yue, W.W. / Hozjan, V. / Cooper, C. / Tumber, A. / Krojer, T. / Muniz, J. / Allerston, C. / Salah, E. / McDonough, M.A. / von Delft, F. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / Bountra, C. / Schofield, C.J. / Kavanagh, K.L. / Oppermann, U.
CitationJournal: FEBS Lett. / Year: 2010
Title: Crystal structure of the PHF8 Jumonji domain, an Nepsilon-methyl lysine demethylase.
Authors: Yue, W.W. / Hozjan, V. / Ge, W. / Loenarz, C. / Cooper, C.D. / Schofield, C.J. / Kavanagh, K.L. / Oppermann, U. / McDonough, M.A.
History
DepositionOct 29, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Mar 28, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_sheet
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHD FINGER PROTEIN 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,35016
Polymers42,9631
Non-polymers1,38715
Water3,027168
1
A: PHD FINGER PROTEIN 8
hetero molecules

A: PHD FINGER PROTEIN 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,69932
Polymers85,9262
Non-polymers2,77330
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation14_655-x+1,-y+1/2,z1
Buried area8090 Å2
ΔGint-218.4 kcal/mol
Surface area31040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.980, 150.980, 150.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-1480-

SO4

21A-2026-

HOH

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Components

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Protein / Sugars , 2 types, 3 molecules A

#1: Protein PHD FINGER PROTEIN 8


Mass: 42963.047 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 115-483
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: Q9UPP1
#5: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 181 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsGENBANK ACCESSION CODE 32698700

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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: 3.36 Å3/Da / Density % sol: 0.63 % / Description: NONE
Crystal growDetails: 1.5 M (NH4)2SO4, 0.1 M SODIUM ACETATE PH 4.25

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.15→106.75 Å / Num. obs: 31194 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 9.7 % / Biso Wilson estimate: 45.54 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.6
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YU1

2yu1


Resolution: 2.15→33.76 Å / SU ML: 0.34 / σ(F): 1.37 / Phase error: 21.33 / Stereochemistry target values: ML
Details: THERE IS DIFFERENCE FO-FC DENSITY AT THE ACTIVE SITE. THE IDENTITY OF THE BOUND LIGAND IS NOT KNOWN, AND HENCE NOT MODELLED.
RfactorNum. reflection% reflection
Rfree0.2115 1582 5.1 %
Rwork0.1754 --
obs0.1773 31106 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.96 Å2 / ksol: 0.361 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.15→33.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2900 0 80 168 3148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083057
X-RAY DIFFRACTIONf_angle_d1.0294143
X-RAY DIFFRACTIONf_dihedral_angle_d16.641080
X-RAY DIFFRACTIONf_chiral_restr0.066465
X-RAY DIFFRACTIONf_plane_restr0.004525
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1503-2.21970.3281560.26912631X-RAY DIFFRACTION100
2.2197-2.2990.28691460.23992668X-RAY DIFFRACTION100
2.299-2.3910.24741430.21072646X-RAY DIFFRACTION100
2.391-2.49980.25931380.19822708X-RAY DIFFRACTION100
2.4998-2.63160.24091490.19272641X-RAY DIFFRACTION100
2.6316-2.79640.27511440.18712688X-RAY DIFFRACTION100
2.7964-3.01210.21231340.1952692X-RAY DIFFRACTION100
3.0121-3.3150.22051390.18022672X-RAY DIFFRACTION100
3.315-3.79420.22131480.16022720X-RAY DIFFRACTION100
3.7942-4.77810.16241490.13082701X-RAY DIFFRACTION100
4.7781-33.76430.15271360.15542757X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.45550.24170.87280.4391-0.10711.3186-0.09210.23590.3245-0.2049-0.12590.0372-0.0230.24670.20630.33610.024-0.12760.3773-0.02340.416555.962745.935910.7862
20.5633-0.34410.33650.4123-0.01130.3786-0.274-0.22740.48990.0194-0.03650.4017-0.109-0.25890.19250.39090.0138-0.29530.4383-0.02620.623443.077151.76219.4966
32.40230.0659-0.22790.55430.03591.335-0.04-0.16750.5269-0.0431-0.05060.2734-0.02910.04870.0730.26240.0112-0.08360.3275-0.05750.43157.604947.395919.5031
40.9471-0.7723-0.15691.0366-0.21381.17130.02990.09930.3755-0.1439-0.15240.10870.19170.33660.10370.30290.0008-0.0990.37940.00250.402362.110347.436110.6387
50.52730.17330.17291.9142-0.40710.81840.1159-0.013-0.08150.1635-0.1526-0.0229-0.09010.06590.04130.2526-0.0139-0.01470.3333-0.06740.329561.720937.884638.1178
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 116:210)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 211:236)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 237:332)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 333:366)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 367:478)

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