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- PDB-2eui: Crystal structure of a probable acetyltransferase -

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Basic information

Entry
Database: PDB / ID: 2eui
TitleCrystal structure of a probable acetyltransferase
ComponentsProbable acetyltransferase
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / transferase / dimer / T1065 / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


N-acetyltransferase activity / acyltransferase activity, transferring groups other than amino-acyl groups
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
Probable acetyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsSwaminathan, S. / Eswaramoorthy, S. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a probable acetyltransferase
Authors: Eswaramoorthy, S. / Swaminathan, S.
History
DepositionOct 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable acetyltransferase
B: Probable acetyltransferase
D: Probable acetyltransferase
E: Probable acetyltransferase


Theoretical massNumber of molelcules
Total (without water)73,0494
Polymers73,0494
Non-polymers00
Water2,468137
1
A: Probable acetyltransferase
B: Probable acetyltransferase


Theoretical massNumber of molelcules
Total (without water)36,5252
Polymers36,5252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-29 kcal/mol
Surface area15360 Å2
MethodPISA
2
D: Probable acetyltransferase
E: Probable acetyltransferase


Theoretical massNumber of molelcules
Total (without water)36,5252
Polymers36,5252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-24 kcal/mol
Surface area15410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.100, 115.100, 66.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein
Probable acetyltransferase


Mass: 18262.301 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Species: Pseudomonas aeruginosa / Strain: PA01 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HX01
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 3.03 Å3/Da / Density % sol: 59.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG 3350, 0.2M Magnesium Chloride, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9805, 0.9802, 0.9400
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 28, 2005
RadiationMonochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.98051
20.98021
30.941
ReflectionResolution: 2.8→50 Å / Num. all: 21842 / Num. obs: 21842 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.6 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 6.6
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.473 / Num. unique all: 2173 / % possible all: 99.7

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Processing

Software
NameVersionClassification
CBASSdata collection
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.8→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.283 823 -RANDOM
Rwork0.227 ---
all-21195 --
obs-21195 97.4 %-
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5015 0 0 137 5152
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0073
X-RAY DIFFRACTIONc_angle_deg1.324

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