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- PDB-3f8k: Crystal structure of protein acetyltransferase (PAT) from Sulfolo... -

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Basic information

Entry
Database: PDB / ID: 3f8k
TitleCrystal structure of protein acetyltransferase (PAT) from Sulfolobus solfataricus
ComponentsProtein acetyltransferase
KeywordsTRANSFERASE / GCN5-related N-acetyltransferase
Function / homology
Function and homology information


N-acetyltransferase activity / cytoplasm
Similarity search - Function
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-acetyltransferase domain-containing protein
Similarity search - Component
Biological speciesSulfolobus solfataricus P2 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.84 Å
AuthorsBrent, M.M.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structure and Biochemical Characterization of Protein Acetyltransferase from Sulfolobus solfataricus.
Authors: Brent, M.M. / Iwata, A. / Carten, J. / Zhao, K. / Marmorstein, R.
History
DepositionNov 12, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5862
Polymers18,8191
Non-polymers7681
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.701, 46.750, 68.624
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 Protein acetyltransferase


Mass: 18818.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus P2 (archaea) / Strain: DSM 1617 / JCM 11322 / P2 / Gene: SSO2813 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q97V23
#2: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 1.91 Å3/Da / Density % sol: 35.44 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 12% PEG 20000, 0.05M MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97932, 0.97945, 0.94932
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 3, 2006 / Details: Adjustable focus K-B pair Si plus Pt, Rh coatings
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979321
20.979451
30.949321
ReflectionResolution: 1.84→30 Å / Num. all: 23855 / Num. obs: 23521 / % possible obs: 98.6 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 23.1
Reflection shellResolution: 1.84→1.92 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 2.5 / % possible all: 89.2

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Processing

Software
NameVersionClassification
MAR345CCDdata collection
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.84→30 Å / Details: The Friedel pairs were used in phasing
RfactorNum. reflection
Rfree0.221 2152
Rwork0.202 -
obs0.202 22938
Solvent computationBsol: 68.0955 Å2 / ksol: 0.415774 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.824 Å20 Å20 Å2
2---0.113 Å20 Å2
3----1.711 Å2
Refinement stepCycle: LAST / Resolution: 1.84→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1053 0 48 73 1174
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.07
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONo_mcbond_it1.4041.5
X-RAY DIFFRACTIONo_mcangle_it2.172
X-RAY DIFFRACTIONo_scbond_it2.542
X-RAY DIFFRACTIONo_scangle_it3.512.5

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