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- PDB-7cmr: The Crystal Structure of human MYST1 from Biortus. -

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Basic information

Entry
Database: PDB / ID: 7cmr
TitleThe Crystal Structure of human MYST1 from Biortus.
ComponentsHistone acetyltransferase KAT8
KeywordsTRANSFERASE / acetyltransferase activity / histone acetyltransferase activity
Function / homology
Function and homology information


MSL complex / histone H4K16 acetyltransferase activity / regulation of mRNA processing / myeloid cell differentiation / NSL complex / : / peptide-lysine-N-acetyltransferase activity / Formation of WDR5-containing histone-modifying complexes / MLL1 complex / histone acetyltransferase complex ...MSL complex / histone H4K16 acetyltransferase activity / regulation of mRNA processing / myeloid cell differentiation / NSL complex / : / peptide-lysine-N-acetyltransferase activity / Formation of WDR5-containing histone-modifying complexes / MLL1 complex / histone acetyltransferase complex / histone acetyltransferase / transcription initiation-coupled chromatin remodeling / neurogenesis / regulation of autophagy / transcription coregulator activity / kinetochore / nuclear matrix / HATs acetylate histones / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / negative regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding / nucleus
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 / Chromo-like domain superfamily ...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
Histone acetyltransferase KAT8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWang, F. / Lin, D. / Lv, Z. / Xu, X. / Tan, J. / Shang, H.
CitationJournal: To Be Published
Title: The Crystal Structure of human MYST1 from Biortus.
Authors: Wang, F. / Lin, D. / Lv, Z. / Xu, X. / Tan, J. / Shang, H.
History
DepositionJul 28, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Structure summary / Category: citation / database_2 / struct
Item: _citation.title / _database_2.pdbx_DOI ..._citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct.title
Revision 1.2Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone acetyltransferase KAT8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6913
Polymers54,5341
Non-polymers1582
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint-1 kcal/mol
Surface area13890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.399, 58.322, 121.120
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 54533.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KAT8, MOF, MYST1, PP7073 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H7Z6, histone acetyltransferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.5 Å3/Da / Density % sol: 18.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M LiCl, 0.1M Hepes pH7, 20% PEG6,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 31, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 16888 / % possible obs: 96.9 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 20.8
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 0.282 / Num. unique obs: 833

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2giv

2giv


Resolution: 2.2→30.476 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.918 / SU B: 5.672 / SU ML: 0.147 / Cross valid method: FREE R-VALUE / ESU R: 0.278 / ESU R Free: 0.222
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2632 804 4.775 %
Rwork0.2178 16035 -
all0.22 --
obs-16839 96.865 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 44.592 Å2
Baniso -1Baniso -2Baniso -3
1--3.214 Å2-0 Å20 Å2
2--3.873 Å2-0 Å2
3----0.66 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30.476 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2163 0 7 62 2232
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0132248
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172061
X-RAY DIFFRACTIONr_angle_refined_deg1.161.6423047
X-RAY DIFFRACTIONr_angle_other_deg1.0611.5774799
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6315262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.45922.685108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.88815386
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.651158
X-RAY DIFFRACTIONr_chiral_restr0.0440.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022440
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02480
X-RAY DIFFRACTIONr_nbd_refined0.1780.2339
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1640.21717
X-RAY DIFFRACTIONr_nbtor_refined0.1620.21035
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0710.2934
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.110.260
X-RAY DIFFRACTIONr_metal_ion_refined0.0220.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.070.22
X-RAY DIFFRACTIONr_nbd_other0.1340.230
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2260.28
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1180.21
X-RAY DIFFRACTIONr_mcbond_it1.444.7651054
X-RAY DIFFRACTIONr_mcbond_other1.4414.7631053
X-RAY DIFFRACTIONr_mcangle_it2.3797.1261314
X-RAY DIFFRACTIONr_mcangle_other2.3787.1281315
X-RAY DIFFRACTIONr_scbond_it1.4384.8421194
X-RAY DIFFRACTIONr_scbond_other1.4384.8421195
X-RAY DIFFRACTIONr_scangle_it2.4587.2031733
X-RAY DIFFRACTIONr_scangle_other2.4577.2031734
X-RAY DIFFRACTIONr_lrange_it3.96751.3412426
X-RAY DIFFRACTIONr_lrange_other3.95751.3212422
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.198-2.2550.262450.2291171X-RAY DIFFRACTION97.9066
2.255-2.3160.278480.2281177X-RAY DIFFRACTION98.7107
2.316-2.3830.253720.2231091X-RAY DIFFRACTION99.4017
2.383-2.4570.27490.2541116X-RAY DIFFRACTION98.8964
2.457-2.5370.305530.2351076X-RAY DIFFRACTION99.9115
2.537-2.6260.32480.2391020X-RAY DIFFRACTION99.2565
2.626-2.7250.24460.2351031X-RAY DIFFRACTION99.7222
2.725-2.8360.27340.237970X-RAY DIFFRACTION99.6032
2.836-2.9620.339470.229925X-RAY DIFFRACTION98.7805
2.962-3.1060.319510.241879X-RAY DIFFRACTION98.3087
3.106-3.2730.314390.236828X-RAY DIFFRACTION97.8555
3.273-3.4710.254460.235792X-RAY DIFFRACTION98.0117
3.471-3.710.232380.209743X-RAY DIFFRACTION97.1393
3.71-4.0060.213520.208660X-RAY DIFFRACTION95.8277
4.006-4.3860.282460.186591X-RAY DIFFRACTION90.099
4.386-4.9010.228210.169525X-RAY DIFFRACTION87.0813
4.901-5.6530.295150.189511X-RAY DIFFRACTION91.0035
5.653-6.9090.266240.22421X-RAY DIFFRACTION91.002
6.909-9.7070.253210.187324X-RAY DIFFRACTION87.1212
9.707-30.4760.20690.206184X-RAY DIFFRACTION79.4239

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