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- PDB-4do0: Crystal Structure of human PHF8 in complex with Daminozide -

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Basic information

Entry
Database: PDB / ID: 4do0
TitleCrystal Structure of human PHF8 in complex with Daminozide
ComponentsHistone lysine demethylase PHF8
KeywordsMETAL BINDING PROTEIN / JMJC DOMAIN / Histone demethylase / Epigenetics / Daminozide / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


histone H4K20 demethylase activity / [histone H3]-dimethyl-L-lysine36 demethylase / histone H3K36me/H3K36me2 demethylase activity / 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 H3]-dimethyl-L-lysine36 demethylase / histone H3K36me/H3K36me2 demethylase activity / 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 / regulation of transcription by RNA polymerase II / nucleolus / 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 ...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 / DAMINOZIDE / Histone lysine demethylase PHF8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsKrojer, T. / Daniel, M. / Ng, S.S. / Walport, L.J. / Chowdhury, R. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Kawamura, A. / Muller-Knapp, S. ...Krojer, T. / Daniel, M. / Ng, S.S. / Walport, L.J. / Chowdhury, R. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Kawamura, A. / Muller-Knapp, S. / McDonough, M.A. / von Delft, F. / Schofield, C.J. / Oppermann, U. / Structural Genomics Consortium (SGC)
History
DepositionFeb 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Database references / Category: reflns / reflns_shell / struct_ref_seq_dif
Item: _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs / _struct_ref_seq_dif.details
Revision 1.2Sep 13, 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: Histone lysine demethylase PHF8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,50814
Polymers43,4021
Non-polymers1,10613
Water66737
1
A: Histone lysine demethylase PHF8
hetero molecules

A: Histone lysine demethylase PHF8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,01628
Polymers86,8032
Non-polymers2,21326
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_555x,-y,-z+1/21
Buried area5940 Å2
ΔGint-166 kcal/mol
Surface area31250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.734, 151.734, 151.734
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Histone lysine demethylase PHF8 / PHD finger protein 8


Mass: 43401.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHF8, KIAA1111, ZNF422 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UPP1

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Non-polymers , 6 types, 50 molecules

#2: Chemical ChemComp-DZA / DAMINOZIDE


Mass: 160.171 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12N2O3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 3.35 Å3/Da / Density % sol: 63.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 4.5
Details: 0.1M acetate, 2M ammonium sulfate, pH 4.5, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.55→107.29 Å / Num. all: 19128 / Num. obs: 19128 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 13.5 % / Biso Wilson estimate: 65.1 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 24.4
Reflection shellResolution: 2.55→2.69 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 4.7 / Num. unique all: 2771 / % possible all: 100

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Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2WWU

2wwu


Resolution: 2.55→107.29 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.911 / SU B: 9.551 / SU ML: 0.208 / Cross valid method: THROUGHOUT / ESU R: 0.377 / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26481 1034 5.4 %RANDOM
Rwork0.20795 ---
all0.21092 18069 --
obs0.21092 18069 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.357 Å2
Refinement stepCycle: LAST / Resolution: 2.55→107.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2875 0 62 37 2974
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.023008
X-RAY DIFFRACTIONr_bond_other_d0.0020.021989
X-RAY DIFFRACTIONr_angle_refined_deg1.5731.9634088
X-RAY DIFFRACTIONr_angle_other_deg0.9633.0014842
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3055366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.15123.926135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.69415484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6141516
X-RAY DIFFRACTIONr_chiral_restr0.080.2462
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213317
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02633
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.445 84 -
Rwork0.321 1282 -
obs--100 %

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