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- PDB-2fia: The crystal structure of the acetyltransferase from Enterococcus ... -

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Basic information

Entry
Database: PDB / ID: 2fia
TitleThe crystal structure of the acetyltransferase from Enterococcus faecalis
Componentsacetyltransferase
KeywordsTRANSFERASE / Acetyltransferase / structural genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


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
: / Acetyltransferase, GNAT family
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsZhang, R. / Zhou, M. / Moy, S. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the acetyltransferase from Enterococcus faecalis
Authors: Zhang, R. / Zhou, M. / Moy, S. / Collart, F. / Joachimiak, A.
History
DepositionDec 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 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
B: acetyltransferase


Theoretical massNumber of molelcules
Total (without water)38,8772
Polymers38,8772
Non-polymers00
Water2,882160
1
A: acetyltransferase


Theoretical massNumber of molelcules
Total (without water)19,4381
Polymers19,4381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: acetyltransferase


Theoretical massNumber of molelcules
Total (without water)19,4381
Polymers19,4381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.679, 79.658, 83.871
Angle α, β, γ (deg.)90.00, 130.54, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein acetyltransferase


Mass: 19438.447 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Gene: GI:29343911 / Plasmid: PDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: GenBank: 29343911, UniProt: Q833M5*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 4 Å3/Da / Density % sol: 69.29 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Bis-Tris, 4M Sodium Nitrate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 287K

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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: Nov 11, 2005 / 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: 2.6→50 Å / Num. all: 18044 / Num. obs: 17923 / % possible obs: 99.33 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 15.8
Reflection shellResolution: 2.6→2.667 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 1.5 / Num. unique all: 1386 / % possible all: 93.07

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collectdata collection
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.917 / SU B: 24.204 / SU ML: 0.222 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.272
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25885 960 5.1 %RANDOM
Rwork0.20971 ---
obs0.21228 17923 99.33 %-
all-18043 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.053 Å2
Baniso -1Baniso -2Baniso -3
1-2.73 Å20 Å20.78 Å2
2---1.83 Å20 Å2
3---0.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.04 Å0.036 Å
Luzzati d res low-6 Å
Luzzati sigma a0.5 Å0.035 Å
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2655 0 0 160 2815
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222719
X-RAY DIFFRACTIONr_bond_other_d0.0010.022444
X-RAY DIFFRACTIONr_angle_refined_deg1.4541.9393653
X-RAY DIFFRACTIONr_angle_other_deg0.82135681
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.2155314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.98823.571140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.32815513
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8211518
X-RAY DIFFRACTIONr_chiral_restr0.090.2382
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022968
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02604
X-RAY DIFFRACTIONr_nbd_refined0.2170.2606
X-RAY DIFFRACTIONr_nbd_other0.1930.22747
X-RAY DIFFRACTIONr_nbtor_refined0.1930.21306
X-RAY DIFFRACTIONr_nbtor_other0.0890.21627
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2540.2128
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3320.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.270.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2990.210
X-RAY DIFFRACTIONr_mcbond_it1.3031.52057
X-RAY DIFFRACTIONr_mcbond_other0.1951.5644
X-RAY DIFFRACTIONr_mcangle_it1.56922532
X-RAY DIFFRACTIONr_scbond_it3.48831375
X-RAY DIFFRACTIONr_scangle_it3.64.51121
X-RAY DIFFRACTIONr_rigid_bond_restr8.12536435
X-RAY DIFFRACTIONr_sphericity_free3.7543160
X-RAY DIFFRACTIONr_sphericity_bonded2.33135099
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 61 -
Rwork0.308 1229 -
obs--93.07 %

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