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- PDB-4ua3: Crystal structure of selenomethionine labeled SpNatD -

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Basic information

Entry
Database: PDB / ID: 4ua3
TitleCrystal structure of selenomethionine labeled SpNatD
ComponentsUncharacterized N-acetyltransferase C825.04c
KeywordsTRANSFERASE / Acetyltransferase / GNAT fold / N-terminal acetylation / acetyl-CoA
Function / homology
Function and homology information


regulation of rDNA heterochromatin formation / N-terminal L-serine Nalpha-acetyltransferase NatD / histone H2A acetyltransferase activity / N-terminal peptidyl-methionine acetylation / : / : / peptide-serine-alpha-N-acetyltransferase activity / N-terminal protein amino acid acetylation / histone H4 acetyltransferase activity / cell division site ...regulation of rDNA heterochromatin formation / N-terminal L-serine Nalpha-acetyltransferase NatD / histone H2A acetyltransferase activity / N-terminal peptidyl-methionine acetylation / : / : / peptide-serine-alpha-N-acetyltransferase activity / N-terminal protein amino acid acetylation / histone H4 acetyltransferase activity / cell division site / nucleus / cytoplasm / cytosol
Similarity search - Function
N-alpha-acetyltransferase 40 / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / N-alpha-acetyltransferase 40
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsMagin, R.S. / Liszczak, G.P. / Marmorstein, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM060293 United States
CitationJournal: Structure / Year: 2015
Title: The Molecular Basis for Histone H4- and H2A-Specific Amino-Terminal Acetylation by NatD.
Authors: Magin, R.S. / Liszczak, G.P. / Marmorstein, R.
History
DepositionAug 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized N-acetyltransferase C825.04c
B: Uncharacterized N-acetyltransferase C825.04c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2555
Polymers46,6852
Non-polymers1,5713
Water4,216234
1
A: Uncharacterized N-acetyltransferase C825.04c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1453
Polymers23,3421
Non-polymers8032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uncharacterized N-acetyltransferase C825.04c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1102
Polymers23,3421
Non-polymers7681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.701, 42.629, 85.417
Angle α, β, γ (deg.)90.00, 98.68, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-409-

HOH

21A-431-

HOH

31A-432-

HOH

41A-443-

HOH

51A-449-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A
211CHAIN B

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Components

#1: Protein Uncharacterized N-acetyltransferase C825.04c


Mass: 23342.291 Da / Num. of mol.: 2 / Fragment: UNP residues 13-204
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / ATCC 24843 / Gene: SPCC825.04c / Production host: Escherichia coli (E. coli)
References: UniProt: Q9USH6, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 2.21 Å3/Da / Density % sol: 44.38 % / Mosaicity: 0.279 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350 and 200 mM potassium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9788 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 1, 2013
RadiationMonochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 34839 / % possible obs: 99.4 % / Redundancy: 17.4 % / Biso Wilson estimate: 27.82 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 12.2
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 16.7 % / Rmerge(I) obs: 0.595 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-3000data collection
HKL-3000data scaling
PDB_EXTRACT3.14data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.85→35.36 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.239 3352 4.97 %
Rwork0.179 --
obs0.182 67462 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.44 Å2
Refinement stepCycle: LAST / Resolution: 1.85→35.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3132 0 97 234 3463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073310
X-RAY DIFFRACTIONf_angle_d1.0784480
X-RAY DIFFRACTIONf_dihedral_angle_d14.1861181
X-RAY DIFFRACTIONf_chiral_restr0.047472
X-RAY DIFFRACTIONf_plane_restr0.005548
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDType
11A1615X-RAY DIFFRACTIONPOSITIONAL
12B1615X-RAY DIFFRACTIONPOSITIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.87840.39391240.27292438X-RAY DIFFRACTION94
1.8784-1.90640.38131370.25462686X-RAY DIFFRACTION98
1.9064-1.93620.29471390.24382650X-RAY DIFFRACTION99
1.9362-1.96790.31571410.21212677X-RAY DIFFRACTION99
1.9679-2.00190.33511360.20722652X-RAY DIFFRACTION99
2.0019-2.03830.3131500.20532768X-RAY DIFFRACTION99
2.0383-2.07750.22611300.19412607X-RAY DIFFRACTION99
2.0775-2.11990.25691420.18872706X-RAY DIFFRACTION99
2.1199-2.1660.33181380.19472662X-RAY DIFFRACTION99
2.166-2.21630.24441450.19332646X-RAY DIFFRACTION100
2.2163-2.27170.38631400.19472750X-RAY DIFFRACTION99
2.2717-2.33320.30861430.19372626X-RAY DIFFRACTION99
2.3332-2.40180.28841360.18542672X-RAY DIFFRACTION100
2.4018-2.47930.25761460.18052702X-RAY DIFFRACTION100
2.4793-2.56790.26551410.1972675X-RAY DIFFRACTION99
2.5679-2.67070.28021420.20282741X-RAY DIFFRACTION100
2.6707-2.79220.30841370.2022668X-RAY DIFFRACTION100
2.7922-2.93930.31371410.19692697X-RAY DIFFRACTION100
2.9393-3.12340.23541390.19232648X-RAY DIFFRACTION100
3.1234-3.36430.26271430.18692708X-RAY DIFFRACTION100
3.3643-3.70260.20971390.16192676X-RAY DIFFRACTION100
3.7026-4.23760.17771430.16062722X-RAY DIFFRACTION100
4.2376-5.3360.19111420.13552696X-RAY DIFFRACTION100
5.336-35.36550.15971380.16812637X-RAY DIFFRACTION98

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