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- PDB-3t9y: Crystal structure of GNAT family acetyltransferase Staphylococcus... -

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Basic information

Entry
Database: PDB / ID: 3t9y
TitleCrystal structure of GNAT family acetyltransferase Staphylococcus aureus subsp. aureus USA300_TCH1516
ComponentsAcetyltransferase, GNAT family
KeywordsTRANSFERASE / PSI-BIOLOGY / Structural genomics / Midwest center for structural genomics / MCSG / acetyltransferase
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
TRIETHYLENE GLYCOL / Acetyltransferase, GNAT family / Acetyltransferase, GNAT family
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsChang, C. / Tesar, C. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of GNAT family acetyltransferase Staphylococcus aureus subsp. aureus USA300_TCH1516
Authors: Chang, C. / Tesar, C. / Jedrzejczak, R. / Joachimiak, A.
History
DepositionAug 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acetyltransferase, GNAT family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1015
Polymers17,7311
Non-polymers3704
Water1,58588
1
A: Acetyltransferase, GNAT family
hetero molecules

A: Acetyltransferase, GNAT family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,20210
Polymers35,4612
Non-polymers7418
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area6570 Å2
ΔGint-35 kcal/mol
Surface area13970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.711, 91.746, 53.866
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-172-

HOH

21A-228-

HOH

Details(x,y,x) and (x,-y+1,-z)

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Components

#1: Protein Acetyltransferase, GNAT family /


Mass: 17730.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: USA300 / Gene: SAUSA300_1980 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q2FF97, UniProt: A0A0H2XI93*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.43 Å3/Da / Density % sol: 49.36 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Lithium sulfate, 0.1M Tris-Cl, 40% PEG400, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97904 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 2, 2011
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97904 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 11945 / Num. obs: 11346 / % possible obs: 95 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 15
Reflection shellResolution: 2→2.03 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2 / Num. unique all: 425 / % possible all: 73.7

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MLPHAREphasing
DMphasing
SHELXDEphasing
RESOLVEphasing
ARP/wARPmodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 8.919 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.182
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2279 464 4.8 %RANDOM
Rwork0.1731 ---
all0.1758 9704 --
obs0.1758 9704 81.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 181.75 Å2 / Biso mean: 35.5671 Å2 / Biso min: 15.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.53 Å20 Å2
3----0.59 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1101 0 23 88 1212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221170
X-RAY DIFFRACTIONr_angle_refined_deg1.2641.9891557
X-RAY DIFFRACTIONr_dihedral_angle_1_deg65139
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.79124.10756
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.72915236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.201158
X-RAY DIFFRACTIONr_chiral_restr0.0870.2165
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02852
X-RAY DIFFRACTIONr_mcbond_it1.7941.5685
X-RAY DIFFRACTIONr_mcangle_it3.23621100
X-RAY DIFFRACTIONr_scbond_it3.0933485
X-RAY DIFFRACTIONr_scangle_it5.1624.5457
X-RAY DIFFRACTIONr_rigid_bond_restr1.63931170
LS refinement shellResolution: 2.003→2.055 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 15 -
Rwork0.174 346 -
all-361 -
obs-361 42.03 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.76740.11240.54130.10130.24810.71850.0274-0.0325-0.04450.0101-0.0042-0.00210.0424-0.0239-0.02320.1615-0.0021-0.00210.11920.00690.137730.164324.19427.476
20.16090.09350.15150.26610.02150.32-0.00040.0210.0114-0.01840.0057-0.00610.01880.0096-0.00520.1570.0009-0.00220.12770.00080.132727.768927.7183-4.4721
30.15380.1059-0.05050.4546-0.09310.22590.014-0.0015-0.01560.024-0.009-0.00070.01230.0165-0.00510.15260.002-0.00260.1323-0.00140.136329.553331.09687.8608
40.01710.00880.00860.2963-0.07840.030.0026-0.00050.00050.014-0.01160.0078-0.0059-0.00880.0090.1553-0.00090.00260.12930.00150.131225.057343.4465.5062
50.0126-0.0309-0.03290.44910.05640.1035-0.00650.01010.0105-0.01150.01220.0154-0.0035-0.0028-0.00580.1548-0.0005-0.00240.12910.00220.133421.717139.98196.421
60.14090.1803-0.06120.3541-0.00780.16950.0086-0.01140.00710.0149-0.002-0.00250.0146-0.0174-0.00660.1583-0.00180.00060.13010.00520.12918.710131.451114.466
71.3988-1.0590.11711.2164-0.1850.44970.01820.0123-0.04870.0626-0.00840.0682-0.0822-0.0566-0.00980.1480.00340.01460.13040.00820.127922.80544.72910.9187
80.2084-0.58890.14611.793-0.44370.110.077-0.2228-0.3215-0.55570.23340.99330.1436-0.083-0.31030.55370.0171-0.35621.31410.1570.55648.873738.80365.5283
90.1437-0.13780.05940.1509-0.18591.21570.0396-0.0082-0.0155-0.01070.02940.022-0.0367-0.11-0.0690.1631-0.0245-0.00370.11620.0050.137913.308746.2761-2.9722
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 22
2X-RAY DIFFRACTION2A23 - 43
3X-RAY DIFFRACTION3A44 - 58
4X-RAY DIFFRACTION4A59 - 72
5X-RAY DIFFRACTION5A73 - 87
6X-RAY DIFFRACTION6A88 - 107
7X-RAY DIFFRACTION7A108 - 118
8X-RAY DIFFRACTION8A119 - 135
9X-RAY DIFFRACTION9A136 - 147

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