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- PDB-2giv: Human MYST histone acetyltransferase 1 -

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Basic information

Entry
Database: PDB / ID: 2giv
TitleHuman MYST histone acetyltransferase 1
ComponentsProbable histone acetyltransferase MYST1
KeywordsTRANSFERASE / histone acetyltransferase / Structural Genomics / Structural Genomics Consortium / SGC
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
N-acetyl transferase-like / 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 / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Chromo/chromo shadow domain ...N-acetyl transferase-like / 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 / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / Gcn5-related N-acetyltransferase (GNAT) / Acyl-CoA N-acyltransferase / Aminopeptidase / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETYL COENZYME *A / : / Histone acetyltransferase KAT8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsMin, J. / Wu, H. / Loppnau, P. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Plotnikov, A.N. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The Crystal Structure of Human MYST histone acetyltransferase 1 in complex with acetylcoenzyme A
Authors: Wu, H. / Min, J. / Loppnau, P. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Plotnikov, A.N.
History
DepositionMar 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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_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.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_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_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
Revision 1.4Nov 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

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Assembly

Deposited unit
A: Probable histone acetyltransferase MYST1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3694
Polymers34,4591
Non-polymers9103
Water3,333185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.305, 58.577, 119.753
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Probable histone acetyltransferase MYST1 / MYST protein 1 / MOZ / YBF2/SAS3 / SAS2 and TIP60 protein 1 / hMOF


Mass: 34458.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYST1, MOF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)codon plus RIL
References: GenBank: 14149875, UniProt: Q9H7Z6*PLUS, 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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.5 Å3/Da / Density % sol: 50.86 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG3350, 0.2 M CaCl2, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 20, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→41.89 Å / Num. all: 22088 / Num. obs: 22088 / % possible obs: 88.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.94→2.02 Å / % possible all: 41

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalClear(MSC/RIGAKU)data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MJB

1mjb


Resolution: 1.94→41.89 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.914 / SU B: 4.781 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.192 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26198 1125 5.1 %RANDOM
Rwork0.20747 ---
all0.21035 20906 --
obs0.21035 20906 88.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.936 Å2
Baniso -1Baniso -2Baniso -3
1--1.8 Å20 Å20 Å2
2--1.85 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.94→41.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2106 0 53 185 2344
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0222219
X-RAY DIFFRACTIONr_angle_refined_deg2.1221.9823017
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.6035257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.43623.85496
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.00715366
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.579158
X-RAY DIFFRACTIONr_chiral_restr0.210.2315
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021663
X-RAY DIFFRACTIONr_nbd_refined0.2410.21057
X-RAY DIFFRACTIONr_nbtor_refined0.3180.21482
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2167
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.28
X-RAY DIFFRACTIONr_mcbond_it1.2491.51335
X-RAY DIFFRACTIONr_mcangle_it1.89822091
X-RAY DIFFRACTIONr_scbond_it2.94831060
X-RAY DIFFRACTIONr_scangle_it4.2654.5926
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 37 -
Rwork0.317 644 -
obs--38.07 %

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