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- PDB-1ufh: Structure of putative acetyltransferase, YYCN protein of Bacillus... -

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Basic information

Entry
Database: PDB / ID: 1ufh
TitleStructure of putative acetyltransferase, YYCN protein of Bacillus subtilis
ComponentsYYCN protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha and beta / fold / acetyltransferase / bacillus subtilis / 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 / 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 subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsTaneja, B. / Maar, S. / Shuvalova, L. / Collart, F.R. / Anderson, W. / Mondragon, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Proteins / Year: 2003
Title: Structure of the bacillus subtilis YYCN protein: a putative N-acetyltransferase
Authors: Taneja, B. / Maar, S. / Shuvalova, L. / Collart, F.R. / Anderson, W. / Mondragon, A.
History
DepositionMay 29, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 24, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Dec 21, 2022Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YYCN protein
B: YYCN protein


Theoretical massNumber of molelcules
Total (without water)41,8692
Polymers41,8692
Non-polymers00
Water1,45981
1
A: YYCN protein
B: YYCN protein

A: YYCN protein
B: YYCN protein


Theoretical massNumber of molelcules
Total (without water)83,7394
Polymers83,7394
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
2
A: YYCN protein

B: YYCN protein


Theoretical massNumber of molelcules
Total (without water)41,8692
Polymers41,8692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556-x+1/2,y+1/2,-z+11
Buried area3850 Å2
ΔGint-16 kcal/mol
Surface area16790 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)87.260, 88.580, 55.800
Angle α, β, γ (deg.)90.00, 98.80, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-159-

HOH

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Components

#1: Protein YYCN protein


Mass: 20934.717 Da / Num. of mol.: 2
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: YYCN / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / References: UniProt: O32293
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.9 Å3/Da / Density % sol: 57.26 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 900mM Ammonium phosphate, 190mM Sodium chloride, 100mM Imidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
15 mg/mlprotein1drop
2900 mMammonium phosphate1reservoir
3190 mM1reservoirNaCl
4100 mMimidazole1reservoirpH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.9792, 0.9565
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 20, 2003
RadiationMonochromator: Silicon mirrors / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.95651
ReflectionResolution: 2.2→26.08 Å / Num. all: 21340 / Num. obs: 21316 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.113 / Rsym value: 0.085 / Net I/σ(I): 6.8
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 18.8 / Rsym value: 0.238 / % possible all: 99.3
Reflection
*PLUS
Highest resolution: 2.2 Å / Num. obs: 21192 / Rmerge(I) obs: 0.085
Reflection shell
*PLUS
Highest resolution: 2.2 Å / % possible obs: 99.3 % / Rmerge(I) obs: 0.238 / Mean I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
REFMAC5refinement
MAR345data collection
XDSdata scaling
SHARPphasing
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→26.08 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.901 / SU B: 7.703 / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.271 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25894 1096 5.1 %RANDOM
Rwork0.23252 ---
all0.258 20220 --
obs0.2339 20220 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.173 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20.1 Å2
2--0.02 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.2→26.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2543 0 0 81 2624
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0212615
X-RAY DIFFRACTIONr_angle_refined_deg1.2551.9393542
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.2033307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.77115476
X-RAY DIFFRACTIONr_chiral_restr0.0860.2376
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021980
X-RAY DIFFRACTIONr_nbd_refined0.2480.31105
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.5186
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2510.395
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.520
X-RAY DIFFRACTIONr_mcbond_it0.6721.51541
X-RAY DIFFRACTIONr_mcangle_it1.29722479
X-RAY DIFFRACTIONr_scbond_it1.99831074
X-RAY DIFFRACTIONr_scangle_it3.2574.51063
LS refinement shellResolution: 2.2→2.318 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.35 151 -
Rwork0.274 2934 -
obs-2934 99.8 %
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.259 / Rfactor Rwork: 0.233
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.012
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.26

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