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- PDB-3qb8: Paramecium Chlorella Bursaria Virus1 Putative ORF A654L is a Poly... -

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Basic information

Entry
Database: PDB / ID: 3qb8
TitleParamecium Chlorella Bursaria Virus1 Putative ORF A654L is a Polyamine Acetyltransferase
ComponentsA654L protein
KeywordsTRANSFERASE / GNAT N-Acetyltransferase / Acetyltransferase / CoA / Spermine / Spermidine
Function / homology
Function and homology information


N-acetyltransferase activity
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 / IMIDAZOLE / N-acetyltransferase domain-containing protein
Similarity search - Component
Biological speciesParamecium bursaria Chlorella virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsCharlop-Powers, Z. / Zhou, M.-M. / Jakoncic, J. / Gurnon, J. / Van Etten, J.
CitationJournal: J. Biol. Chem. / Year: 2012
Title: Paramecium bursaria chlorella virus 1 encodes a polyamine acetyltransferase.
Authors: Charlop-Powers, Z. / Jakoncic, J. / Gurnon, J.R. / Van Etten, J.L. / Zhou, M.M.
History
DepositionJan 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: A654L protein
B: A654L protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5166
Polymers44,8432
Non-polymers1,6734
Water7,512417
1
A: A654L protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2583
Polymers22,4211
Non-polymers8372
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: A654L protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2583
Polymers22,4211
Non-polymers8372
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.400, 65.400, 112.631
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein A654L protein


Mass: 22421.385 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paramecium bursaria Chlorella virus 1 / Gene: A654L / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O41136
#2: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 417 / 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: 3.1 Å3/Da / Density % sol: 60.34 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 0.9 M Sodium Citrate, 0.1M Imidizole pH 8.0, 0.1M Glycine-NaOH pH 10.5, 15% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X6A11.7
SYNCHROTRONNSLS X6A21
Detector
TypeIDDetectorDate
MAR CCD 130 mm1CCDAug 12, 2010
MAR CCD 130 mm2CCDOct 12, 2010
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1siliconSINGLE WAVELENGTHMx-ray1
2siliconSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.71
211
ReflectionResolution: 1.4→50 Å / Num. all: 106656 / Num. obs: 106487

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Processing

Software
NameClassification
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→28.278 Å / SU ML: 0.17 / σ(F): 1.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.168 4333 5.03 %
Rwork0.1518 --
obs0.1526 86178 99.84 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.222 Å2 / ksol: 0.409 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.5238 Å2-0 Å20 Å2
2--0.5238 Å2-0 Å2
3---1.8277 Å2
Refinement stepCycle: LAST / Resolution: 1.5→28.278 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3134 0 106 417 3657
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0173464
X-RAY DIFFRACTIONf_angle_d1.6934739
X-RAY DIFFRACTIONf_dihedral_angle_d16.0951368
X-RAY DIFFRACTIONf_chiral_restr0.365527
X-RAY DIFFRACTIONf_plane_restr0.009594
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.55360.2384590.21088218X-RAY DIFFRACTION100
1.5536-1.61580.23014170.19358191X-RAY DIFFRACTION100
1.6158-1.68940.21434340.16578173X-RAY DIFFRACTION100
1.6894-1.77840.19274260.15218196X-RAY DIFFRACTION100
1.7784-1.88980.16474400.13888175X-RAY DIFFRACTION100
1.8898-2.03570.16024430.13248197X-RAY DIFFRACTION100
2.0357-2.24050.16184240.13728201X-RAY DIFFRACTION100
2.2405-2.56450.15014330.1478166X-RAY DIFFRACTION100
2.5645-3.23030.16054370.16028198X-RAY DIFFRACTION100
3.2303-28.28350.16054200.1498130X-RAY DIFFRACTION99

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