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- PDB-2i00: Crystal structure of acetyltransferase (GNAT family) from Enteroc... -

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Basic information

Entry
Database: PDB / ID: 2i00
TitleCrystal structure of acetyltransferase (GNAT family) from Enterococcus faecalis
ComponentsAcetyltransferase, GNAT family
KeywordsTRANSFERASE / acetyltransferase / GNAT family / structural genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


aminoglycoside antibiotic catabolic process / aminoglycoside N-acetyltransferase activity
Similarity search - Function
Enhanced intracellular survival protein domain / Eis-like, acetyltransferase domain / : / Sterol carrier protein domain / Acetyltransferase (GNAT) domain / SCP2 sterol-binding domain / Acetyltransferase (GNAT) domain / Nonspecific Lipid-transfer Protein; Chain A / SCP2 sterol-binding domain superfamily / Gcn5-related N-acetyltransferase (GNAT) ...Enhanced intracellular survival protein domain / Eis-like, acetyltransferase domain / : / Sterol carrier protein domain / Acetyltransferase (GNAT) domain / SCP2 sterol-binding domain / Acetyltransferase (GNAT) domain / Nonspecific Lipid-transfer Protein; Chain A / SCP2 sterol-binding domain superfamily / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Acetyltransferase, GNAT family
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsZhang, R. / Zhou, M. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published / Year: 2006
Title: The crystal structure of the acetyltransferase (GNAT family) from Enterococcus faecalis
Authors: Zhang, R. / Zhou, M. / Moy, S. / Joachimiak, A.
History
DepositionAug 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetyltransferase, GNAT family
B: Acetyltransferase, GNAT family
C: Acetyltransferase, GNAT family
D: Acetyltransferase, GNAT family
E: Acetyltransferase, GNAT family
F: Acetyltransferase, GNAT family


Theoretical massNumber of molelcules
Total (without water)288,4636
Polymers288,4636
Non-polymers00
Water6,774376
1
A: Acetyltransferase, GNAT family
B: Acetyltransferase, GNAT family


Theoretical massNumber of molelcules
Total (without water)96,1542
Polymers96,1542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-10 kcal/mol
Surface area33290 Å2
MethodPISA, PQS
2
C: Acetyltransferase, GNAT family
D: Acetyltransferase, GNAT family


Theoretical massNumber of molelcules
Total (without water)96,1542
Polymers96,1542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-7 kcal/mol
Surface area33270 Å2
MethodPISA, PQS
3
E: Acetyltransferase, GNAT family
F: Acetyltransferase, GNAT family


Theoretical massNumber of molelcules
Total (without water)96,1542
Polymers96,1542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-7 kcal/mol
Surface area33490 Å2
MethodPISA, PQS
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16860 Å2
ΔGint-42 kcal/mol
Surface area92660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.410, 177.091, 104.429
Angle α, β, γ (deg.)90.00, 94.89, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThis protein exists as dimer. Molecules A and B, molecules C and D, molecules E and F are three dimers in the asymmetric unit.

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Components

#1: Protein
Acetyltransferase, GNAT family


Mass: 48077.145 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Gene: EF_2353 / Plasmid: PDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q831Y9, amino-acid N-acetyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / 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: 2.47 Å3/Da / Density % sol: 50.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2M Tri-sodium citrate dihydrate, 20% PEG3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 20, 2006 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 117708 / Num. obs: 116355 / % possible obs: 98.85 % / Observed criterion σ(F): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 52 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.06
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1 / % possible all: 89.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.3→41.92 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.914 / SU B: 18.876 / SU ML: 0.223 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.381 / ESU R Free: 0.265
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26977 6179 5 %RANDOM
Rwork0.21301 ---
all0.21582 116355 --
obs0.21582 116355 98.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.709 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å2-0.76 Å2
2---0.2 Å20 Å2
3----0.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.042 Å0.034 Å
Luzzati d res low-6 Å
Luzzati sigma a0.5 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.3→41.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19902 0 0 376 20278
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02220541
X-RAY DIFFRACTIONr_bond_other_d0.0010.0217874
X-RAY DIFFRACTIONr_angle_refined_deg1.451.93427906
X-RAY DIFFRACTIONr_angle_other_deg0.879341595
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.99452381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.56724.3031127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.155153388
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.01815108
X-RAY DIFFRACTIONr_chiral_restr0.0920.22891
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0222927
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024493
X-RAY DIFFRACTIONr_nbd_refined0.2060.24210
X-RAY DIFFRACTIONr_nbd_other0.1890.219061
X-RAY DIFFRACTIONr_nbtor_refined0.1860.29672
X-RAY DIFFRACTIONr_nbtor_other0.090.211939
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2653
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.060.23
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2260.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2640.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9621.515381
X-RAY DIFFRACTIONr_mcbond_other0.121.54780
X-RAY DIFFRACTIONr_mcangle_it1.074219378
X-RAY DIFFRACTIONr_scbond_it1.478310417
X-RAY DIFFRACTIONr_scangle_it2.1954.58528
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 394 -
Rwork0.287 7828 -
obs--89.73 %
Refinement TLS params.Method: refined / Origin x: 44.9728 Å / Origin y: 26.1278 Å / Origin z: 126.1672 Å
111213212223313233
T-0.077 Å20.0093 Å2-0.0214 Å2--0.0522 Å20.0263 Å2---0.0485 Å2
L0.1378 °2-0.0267 °2-0.0335 °2-0.1657 °20.0086 °2--0.1529 °2
S0.0171 Å °0.0349 Å °-0.009 Å °0.0215 Å °-0.0296 Å °-0.0135 Å °-0.0087 Å °-0.0197 Å °0.0126 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA10 - 15010 - 150
2X-RAY DIFFRACTION1AA151 - 300151 - 300
3X-RAY DIFFRACTION1AA301 - 406301 - 406
4X-RAY DIFFRACTION1BB11 - 15011 - 150
5X-RAY DIFFRACTION1BB151 - 300151 - 300
6X-RAY DIFFRACTION1BB301 - 406301 - 406
7X-RAY DIFFRACTION1CC9 - 1509 - 150
8X-RAY DIFFRACTION1CC151 - 300151 - 300
9X-RAY DIFFRACTION1CC301 - 406301 - 406
10X-RAY DIFFRACTION1DD11 - 15011 - 150
11X-RAY DIFFRACTION1DD151 - 300151 - 300
12X-RAY DIFFRACTION1DD301 - 406301 - 406
13X-RAY DIFFRACTION1EE11 - 15011 - 150
14X-RAY DIFFRACTION1EE151 - 300151 - 300
15X-RAY DIFFRACTION1EE301 - 406301 - 406
16X-RAY DIFFRACTION1FF9 - 1509 - 150
17X-RAY DIFFRACTION1FF151 - 300151 - 300
18X-RAY DIFFRACTION1FF301 - 406301 - 406

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