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- PDB-5wci: Human MYST histone acetyltransferase 1 -

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Basic information

Entry
Database: PDB / ID: 5wci
TitleHuman MYST histone acetyltransferase 1
ComponentsHistone acetyltransferase KAT8
KeywordsTRANSFERASE / MOF / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


positive regulation of skeletal muscle satellite cell differentiation / regulation of mitochondrial transcription / MSL complex / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K16 acetyltransferase activity / protein propionyltransferase activity / regulation of mRNA processing / histone H4 acetyltransferase activity / myeloid cell differentiation ...positive regulation of skeletal muscle satellite cell differentiation / regulation of mitochondrial transcription / MSL complex / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K16 acetyltransferase activity / protein propionyltransferase activity / regulation of mRNA processing / histone H4 acetyltransferase activity / myeloid cell differentiation / post-embryonic hemopoiesis / NSL complex / negative regulation of epithelial to mesenchymal transition / peptide-lysine-N-acetyltransferase activity / negative regulation of type I interferon production / oogenesis / NuA4 histone acetyltransferase complex / Formation of WDR5-containing histone-modifying complexes / MLL1 complex / histone acetyltransferase complex / positive regulation of transcription initiation by RNA polymerase II / histone acetyltransferase / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / neurogenesis / transcription initiation-coupled chromatin remodeling / regulation of autophagy / transcription coregulator activity / kinetochore / nuclear matrix / chromosome / HATs acetylate histones / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / negative regulation of DNA-templated transcription / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / mitochondrion / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
: / MYST, zinc finger domain / MYST family zinc finger domain / Histone acetyltransferase domain, MYST-type / MOZ/SAS family / MYST-type histone acetyltransferase (HAT) domain profile. / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / Chromo/chromo shadow domain / Chromatin organization modifier domain ...: / MYST, zinc finger domain / MYST family zinc finger domain / Histone acetyltransferase domain, MYST-type / MOZ/SAS family / MYST-type histone acetyltransferase (HAT) domain profile. / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / Acyl-CoA N-acyltransferase / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
propionyl Coenzyme A / Histone acetyltransferase KAT8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsDong, A. / Zeng, H. / Walker, J.R. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Zheng, Y.G. / Brown, P.J. / Wu, H. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Human MYST histone acetyltransferase 1
Authors: Zeng, H. / Dong, A. / Walker, J.R. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Zheng, Y.G. / Brown, P.J. / Wu, H. / Structural Genomics Consortium (SGC)
History
DepositionJun 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone acetyltransferase KAT8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6318
Polymers34,4591
Non-polymers1,1737
Water4,270237
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint3 kcal/mol
Surface area14660 Å2
Unit cell
Length a, b, c (Å)46.336, 58.729, 120.277
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Histone acetyltransferase KAT8 / Lysine acetyltransferase 8 / MOZ / YBF2/SAS3 / SAS2 and TIP60 protein 1 / hMOF


Mass: 34458.625 Da / Num. of mol.: 1 / Fragment: residues 174-449
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KAT8, MOF, MYST1, PP7073 / Plasmid: pET28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) codon plus RIL / References: UniProt: Q9H7Z6, histone acetyltransferase

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Non-polymers , 5 types, 244 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-1VU / propionyl Coenzyme A


Mass: 823.597 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H40N7O17P3S
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.38 Å3/Da / Density % sol: 48.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 20% PEG 3350, 0.2 M Na malonate pH5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Mar 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 31768 / % possible obs: 98.7 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.026 / Rrim(I) all: 0.097 / Χ2: 0.885 / Net I/σ(I): 7.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.78-1.818.10.91615060.7010.3270.9760.74697.6
1.81-1.8410.80.8610.8340.2680.9030.73596.1
1.84-1.8812.30.7190.9040.210.750.75298.1
1.88-1.9212.90.5710.9350.1620.5940.77997.2
1.92-1.9613.20.4930.9480.1390.5130.79598.2
1.96-213.30.4120.9630.1150.4280.7897.5
2-2.0513.30.3310.9760.0920.3430.81498.9
2.05-2.1113.30.2730.9830.0770.2840.8797.4
2.11-2.1713.50.2420.9870.0670.2520.84699.8
2.17-2.2413.80.2110.9890.0580.2190.87998.3
2.24-2.3213.90.1890.9920.0520.1960.88498.6
2.32-2.42140.1710.9940.0470.1780.8699.9
2.42-2.5314.10.150.9950.0410.1560.88999.2
2.53-2.6614.20.1360.9950.0370.1410.94799.4
2.66-2.8314.20.1060.9970.0290.110.93699.7
2.83-3.0414.10.0790.9980.0220.0820.93399.8
3.04-3.35140.0560.9990.0150.0580.94399.9
3.35-3.8314.10.04410.0120.0461.105100
3.83-4.8313.80.03710.010.0381.107100
4.83-5012.70.03410.010.0350.92298.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
SCALEPACKdata scaling
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GIV

2giv


Resolution: 1.78→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.371 / SU ML: 0.074 / SU R Cruickshank DPI: 0.1248 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.119
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2183 1648 5.2 %RANDOM
Rwork0.1826 ---
obs0.1845 30055 98.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 75.61 Å2 / Biso mean: 24.099 Å2 / Biso min: 10.96 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å2-0 Å20 Å2
2--0.58 Å2-0 Å2
3---0.14 Å2
Refinement stepCycle: final / Resolution: 1.78→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2283 0 70 242 2595
Biso mean--27.05 31.47 -
Num. residues----284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192540
X-RAY DIFFRACTIONr_bond_other_d0.0020.022261
X-RAY DIFFRACTIONr_angle_refined_deg1.3441.9613466
X-RAY DIFFRACTIONr_angle_other_deg0.90335274
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9095307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.09724.074108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.83915408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.674158
X-RAY DIFFRACTIONr_chiral_restr0.0840.2358
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212875
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02527
LS refinement shellResolution: 1.781→1.828 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.438 115 -
Rwork0.345 2101 -
all-2216 -
obs--95.35 %

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