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- PDB-2fsr: Crystal Structure of the Acetyltransferase from Agrobacterium tum... -

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Basic information

Entry
Database: PDB / ID: 2fsr
TitleCrystal Structure of the Acetyltransferase from Agrobacterium tumefaciens str. C58
Componentsacetyltransferase
KeywordsTRANSFERASE / alpha-beta-sandwich / 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) domain / 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
FORMIC ACID / DI(HYDROXYETHYL)ETHER / Acetyltranferase / :
Similarity search - Component
Biological speciesAgrobacterium tumefaciens str. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.52 Å
AuthorsKim, Y. / Joachimiak, A. / Xu, X. / Gu, J. / Edwards, A. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of the Acetyltransferase from Agrobacterium tumefaciens str. C58
Authors: Kim, Y. / Joachimiak, A. / Xu, X. / Gu, J. / Edwards, A. / Savchenko, A.
History
DepositionJan 23, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0323
Polymers21,8801
Non-polymers1522
Water3,891216
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.468, 106.778, 42.099
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-495-

HOH

21A-513-

HOH

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Components

#1: Protein acetyltransferase


Mass: 21879.713 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria)
Species: Agrobacterium tumefaciens / Strain: C58 / Gene: atu2435 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q8UCP8, UniProt: A9CHU9*PLUS
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.3 Å3/Da / Density % sol: 46.44 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M Bis-tris, 0.2M NH4(OAC), 25% PEG3350, 4% Jeffamine M-600, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97912 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 20, 2005 / Details: mirrors
RadiationMonochromator: double crystal monochromator, S1(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
ReflectionResolution: 1.52→35.88 Å / Num. all: 31098 / Num. obs: 30447 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.9 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 12.8
Reflection shellResolution: 1.52→1.57 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 4.97 / Num. unique all: 2511 / % possible all: 81.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
MLPHAREphasing
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.52→35.88 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.946 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19935 2955 10.1 %RANDOM
Rwork0.17942 ---
all0.18147 26368 --
obs0.18147 26368 93.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.351 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å20 Å20 Å2
2---0.38 Å20 Å2
3----0.57 Å2
Refinement stepCycle: LAST / Resolution: 1.52→35.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1344 0 10 216 1570
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211561
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.221.9542137
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5665200
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.68322.53279
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.61215231
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9541516
X-RAY DIFFRACTIONr_chiral_restr0.0780.2214
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021282
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.2702
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21043
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2186
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2160.284
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2640.256
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7531.5949
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.27621534
X-RAY DIFFRACTIONr_scbond_it1.5523612
X-RAY DIFFRACTIONr_scangle_it2.1964.5603
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.523→1.563 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 169 -
Rwork0.217 1483 -
obs-1483 71.92 %

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