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- PDB-1on0: Crystal Structure of Putative Acetyltransferase (YycN) from Bacil... -

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Basic information

Entry
Database: PDB / ID: 1on0
TitleCrystal Structure of Putative Acetyltransferase (YycN) from Bacillus subtilis, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET SR144
ComponentsYycN protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta protein with anti-parallel beta strands / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups / Transferases; Acyltransferases; Transferring groups other than aminoacyl 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
Uncharacterized N-acetyltransferase YycN
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsForouhar, F. / Shen, J. / Kuzin, A. / Chiang, Y. / Xiao, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of Putative Acetyltransferase (YycN) from Bacillus subtilis
Authors: Forouhar, F. / Shen, J. / Kuzin, A. / Chiang, Y. / Xiao, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L.
History
DepositionFeb 26, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YycN protein
B: YycN protein
C: YycN protein
D: YycN protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0909
Polymers74,6704
Non-polymers4205
Water6,431357
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: YycN protein
hetero molecules

D: YycN protein
hetero molecules

A: YycN protein
C: YycN protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0909
Polymers74,6704
Non-polymers4205
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation2_647-x+1,y-1/2,-z+21
identity operation1_555x,y,z1
Buried area11120 Å2
ΔGint-113 kcal/mol
Surface area31950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.891, 101.594, 62.120
Angle α, β, γ (deg.)90, 97, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
YycN protein


Mass: 18667.529 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: YYCN / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O32293
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 357 / 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: 2.5 Å3/Da / Density % sol: 50.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 5mM Tris, 20% PEG 8k, 0.2 M Ammonium Sulfate, 50 mM Sodium Chloride, and 5 mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.982 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 3, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.982 Å / Relative weight: 1
ReflectionResolution: 2.2→29.68 Å / Num. all: 76470 / Num. obs: 69770 / % possible obs: 91.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.26 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.069 / Net I/σ(I): 16.64
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 3.74 / Num. unique all: 2778 / Rsym value: 0.287 / % possible all: 99.1

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: SAD / Resolution: 2.2→29.68 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.289 6881 -random
Rwork0.225 ---
all0.331 69770 --
obs0.259 69770 9.9 %-
Displacement parametersBiso mean: 35.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å28.17 Å2
2---5.48 Å20 Å2
3---4.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.2→29.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5150 0 21 357 5528
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.81
LS refinement shellResolution: 2.2→29.68 Å / Rfactor Rfree error: 0.003
RfactorNum. reflection% reflection
Rfree0.289 6881 -
Rwork0.225 --
obs-69770 9.9 %

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