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- PDB-1yvk: Crystal Structure of the Bacillis subtilis Acetyltransferase in c... -

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Basic information

Entry
Database: PDB / ID: 1yvk
TitleCrystal Structure of the Bacillis subtilis Acetyltransferase in complex with CoA, Northeast Structural Genomics Target SR237.
Componentshypothetical protein BSU33890Hypothesis
KeywordsTRANSFERASE / alphs-beta protein / Structural Genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


N-acetyltransferase activity / 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
COENZYME A / Uncharacterized N-acetyltransferase YvbK
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.01 Å
AuthorsForouhar, F. / Yong, W. / Xiao, R. / Ciano, M. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of the Bacillis subtilis Acetyltransferase in complex with CoA, Northeast Structural Genomics Target SR237.
Authors: Forouhar, F. / Yong, W. / Xiao, R. / Ciano, M. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionFeb 15, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein BSU33890
B: hypothetical protein BSU33890
C: hypothetical protein BSU33890
D: hypothetical protein BSU33890
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,9828
Polymers75,9124
Non-polymers3,0704
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.596, 124.425, 216.942
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
hypothetical protein BSU33890 / Hypothesis


Mass: 18978.080 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Species: Bacillus subtilis / Strain: subsp. subtilis str. 168 / Gene: yvbK / Plasmid: BL21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic
Keywords: Met substitution by Selno-Met and addition of C-tag (LEHHHHHH). YvbK
References: UniProt: O32248
#2: Chemical
ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S

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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: 2.83 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris-HCl (pH 8.5), 20% PEG 4K, 200 mM sodium acetate, 100 mM ammonium sulfate, 2 mM Acetyl-CoA, and 5 mM DTT., VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97927 / Wavelength: 0.97927 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 7, 2005 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. all: 29334 / Num. obs: 29334 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 42.1 Å2 / Rmerge(I) obs: 0.108 / Rsym value: 0.075 / Net I/σ(I): 14.01
Reflection shellResolution: 3→3.11 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 2.32 / Num. unique all: 2388 / Rsym value: 0.343 / % possible all: 77.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 3.01→30 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 128262.73 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.284 2280 9.7 %RANDOM
Rwork0.243 ---
all0.25 29334 --
obs0.243 23509 76.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.275366 e/Å3
Displacement parametersBiso mean: 61.5 Å2
Baniso -1Baniso -2Baniso -3
1-44.32 Å20 Å20 Å2
2---11.56 Å20 Å2
3----32.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.45 Å
Luzzati d res low-5 Å
Luzzati sigma a0.87 Å0.79 Å
Refinement stepCycle: LAST / Resolution: 3.01→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4884 0 192 0 5076
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.62
LS refinement shellResolution: 3.01→3.19 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.392 170 8.6 %
Rwork0.382 1799 -
obs-2280 38.1 %

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