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- PDB-2f6n: Crystal structure of PHD finger-linker-bromodomain fragment of hu... -

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Basic information

Entry
Database: PDB / ID: 2f6n
TitleCrystal structure of PHD finger-linker-bromodomain fragment of human BPTF in the free form
Componentsbromodomain PHD finger transcription factor
KeywordsTRANSCRIPTION / phd finger / bromo domain / histone tail binding / methylation
Function / homology
Function and homology information


NURF complex / endoderm development / anterior/posterior pattern specification / ATPase complex / embryonic placenta development / methylated histone binding / cellular response to nerve growth factor stimulus / brain development / cell body / sequence-specific DNA binding ...NURF complex / endoderm development / anterior/posterior pattern specification / ATPase complex / embryonic placenta development / methylated histone binding / cellular response to nerve growth factor stimulus / brain development / cell body / sequence-specific DNA binding / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / dendrite / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Nucleosome-remodeling factor subunit BPTF / DDT domain / DDT domain / WHIM2 domain / Williams-Beuren syndrome DDT (WSD), D-TOX E motif / DDT domain profile. / domain in different transcription and chromosome remodeling factors / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, PHD-type, conserved site ...Nucleosome-remodeling factor subunit BPTF / DDT domain / DDT domain / WHIM2 domain / Williams-Beuren syndrome DDT (WSD), D-TOX E motif / DDT domain profile. / domain in different transcription and chromosome remodeling factors / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Bromodomain-like / Histone Acetyltransferase; Chain A / Zinc finger, FYVE/PHD-type / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Nucleosome-remodeling factor subunit BPTF / Nucleosome-remodeling factor subunit BPTF
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsLi, H. / Patel, D.J.
CitationJournal: Nature / Year: 2006
Title: Molecular basis for site-specific read-out of histone H3K4me3 by the BPTF PHD finger of NURF.
Authors: Li, H. / Ilin, S. / Wang, W. / Duncan, E.M. / Wysocka, J. / Allis, C.D. / Patel, D.J.
History
DepositionNov 29, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_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_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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: bromodomain PHD finger transcription factor
B: bromodomain PHD finger transcription factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3256
Polymers41,0632
Non-polymers2624
Water5,927329
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.144, 144.894, 38.315
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein bromodomain PHD finger transcription factor


Mass: 20531.531 Da / Num. of mol.: 2 / Fragment: finger-linker-bromodomain (residues 2583-2751)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BPTF / Plasmid: pGex6p / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 / References: UniProt: Q7Z7D6, UniProt: Q12830*PLUS
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.88 Å3/Da / Density % sol: 57.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG 400, 0.1M Tris 8.5, 0.1M KCl, 10mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9797 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 7, 2005
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 32863 / Num. obs: 32535 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 12.6 % / Rmerge(I) obs: 0.105 / Χ2: 1.787
Reflection shellResolution: 2→2.07 Å / Redundancy: 13.1 % / Rmerge(I) obs: 0.476 / Num. unique all: 3175 / Χ2: 0.982 / % possible all: 98.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.234 2576 7.8 %Random
Rwork0.217 ---
all-32959 --
obs-31773 96.4 %-
Solvent computationBsol: 43.701 Å2
Displacement parametersBiso mean: 26.18 Å2
Baniso -1Baniso -2Baniso -3
1-3.019 Å20 Å20 Å2
2---4.553 Å20 Å2
3---1.534 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.12 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2720 0 4 329 3053
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.08
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_dihedral_angle_d20.68
X-RAY DIFFRACTIONc_improper_angle_d0.73
LS refinement shellResolution: 2→2.07 Å /
RfactorNum. reflection
Rfree0.24 237
Rwork0.22 -
obs-3048
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param

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