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- PDB-5ye4: Crystal structure of the complex of di-acetylated histone H4 and ... -

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Basic information

Entry
Database: PDB / ID: 5ye4
TitleCrystal structure of the complex of di-acetylated histone H4 and 1A9D7 Fab fragment
Components
  • 1A9D7 L chain
  • 1A9D7 VH CH1 chain
  • di-acetylated histone H4
KeywordsNUCLEAR PROTEIN / Antibody / Histone / Complex
Function / homology
Function and homology information


arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / lipoxygenase pathway / arachidonate metabolic process / lipid oxidation / hepoxilin biosynthetic process / linoleic acid metabolic process / metal ion binding
Similarity search - Function
Lipoxygenase, iron binding site / Lipoxygenases iron-binding region signature 1. / Lipoxygenase / Lipoxygenase, C-terminal / Lipoxigenase, C-terminal domain superfamily / Lipoxygenase / Lipoxygenase iron-binding catalytic domain profile. / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Arachidonate 15-lipoxygenase
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.799 Å
AuthorsMatsuda, T. / Ito, T. / Wakamori, M. / Umehara, T.
CitationJournal: Epigenetics / Year: 2018
Title: JQ1 affects BRD2-dependent and independent transcription regulation without disrupting H4-hyperacetylated chromatin states.
Authors: Handoko, L. / Kaczkowski, B. / Hon, C.C. / Lizio, M. / Wakamori, M. / Matsuda, T. / Ito, T. / Jeyamohan, P. / Sato, Y. / Sakamoto, K. / Yokoyama, S. / Kimura, H. / Minoda, A. / Umehara, T.
History
DepositionSep 15, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 22, 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_conn_type
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_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 1A9D7 VH CH1 chain
B: 1A9D7 L chain
C: 1A9D7 VH CH1 chain
D: 1A9D7 L chain
E: di-acetylated histone H4
F: di-acetylated histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,83232
Polymers95,1326
Non-polymers1,70126
Water14,214789
1
A: 1A9D7 VH CH1 chain
B: 1A9D7 L chain
E: di-acetylated histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,48217
Polymers47,5663
Non-polymers91614
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6310 Å2
ΔGint-433 kcal/mol
Surface area18640 Å2
MethodPISA
2
C: 1A9D7 VH CH1 chain
D: 1A9D7 L chain
F: di-acetylated histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,35115
Polymers47,5663
Non-polymers78512
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-366 kcal/mol
Surface area18840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.346, 164.093, 73.700
Angle α, β, γ (deg.)90.00, 104.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody 1A9D7 VH CH1 chain


Mass: 22632.248 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#2: Antibody 1A9D7 L chain


Mass: 23746.260 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Protein/peptide di-acetylated histone H4


Mass: 1187.353 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P62805*PLUS
#4: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 789 / 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: 2.42 Å3/Da / Density % sol: 49.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100mM imidazole (pH 6.5), 150 mM zinc acetate, and 17.5% (w/v) PEG3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 287775 / % possible obs: 99 % / Redundancy: 3.5 % / Net I/σ(I): 28.3
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.1 % / Rsym value: 0.334 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FJ1

1fj1


Resolution: 1.799→37.761 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2242 2014 2.44 %
Rwork0.1936 --
obs0.1944 82524 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.799→37.761 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6599 0 26 789 7414
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036769
X-RAY DIFFRACTIONf_angle_d0.719208
X-RAY DIFFRACTIONf_dihedral_angle_d9.9354024
X-RAY DIFFRACTIONf_chiral_restr0.0471018
X-RAY DIFFRACTIONf_plane_restr0.0041175
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7991-1.84410.30611310.25875455X-RAY DIFFRACTION95
1.8441-1.89390.261490.2355627X-RAY DIFFRACTION97
1.8939-1.94970.25491420.21255666X-RAY DIFFRACTION97
1.9497-2.01260.21181430.20215647X-RAY DIFFRACTION98
2.0126-2.08450.2621420.20085792X-RAY DIFFRACTION99
2.0845-2.1680.23021400.19615753X-RAY DIFFRACTION99
2.168-2.26660.22781480.19075743X-RAY DIFFRACTION100
2.2666-2.38610.22441390.19625813X-RAY DIFFRACTION100
2.3861-2.53560.23371510.19475820X-RAY DIFFRACTION100
2.5356-2.73130.25231460.19895830X-RAY DIFFRACTION100
2.7313-3.00610.20951500.19095840X-RAY DIFFRACTION100
3.0061-3.44080.20691400.17925800X-RAY DIFFRACTION100
3.4408-4.3340.1971500.17315865X-RAY DIFFRACTION100
4.334-37.76910.21861430.19545859X-RAY DIFFRACTION100

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