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- PDB-3dsb: The crystal structure of a possible acetyltransferase from Clostr... -

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Basic information

Entry
Database: PDB / ID: 3dsb
TitleThe crystal structure of a possible acetyltransferase from Clostridium difficile 630
ComponentsPutative acetyltransferase
KeywordsTRANSFERASE / APC60368.2 / acetyltransferase / Clostridium difficile 630 / structural genomics / PSI-2 / 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) 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
TRIMETHYL GLYCINE / GCN5-related N-acetyltransferase-like protein
Similarity search - Component
Biological speciesClostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.48 Å
AuthorsTan, K. / Shackelford, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a possible acetyltransferase from Clostridium difficile 630
Authors: Tan, K. / Shackelford, G. / Joachimiak, A.
History
DepositionJul 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative acetyltransferase
B: Putative acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7926
Polymers38,3632
Non-polymers4284
Water7,764431
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6970 Å2
ΔGint-52 kcal/mol
Surface area15730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.488, 66.765, 133.884
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsAuthors state that the biological unit is experimentally unknown. The chains A and B are expected to form a dimer.

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Components

#1: Protein Putative acetyltransferase


Mass: 19181.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium difficile (bacteria) / Strain: 630 / Gene: CD2162 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q185U9
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-BET / TRIMETHYL GLYCINE


Mass: 118.154 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 431 / 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: 2.42 Å3/Da / Density % sol: 49.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 0.1M Ammonium Sulfate 0.1M Tris-Sodium Citrate, pH 4, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97932 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 20, 2008 / Details: Mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 1.48→37.1 Å / Num. all: 62315 / Num. obs: 62315 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 42.4
Reflection shellResolution: 1.48→1.51 Å / Redundancy: 6 % / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 4 / Num. unique all: 2787 / % possible all: 90.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.48→37.1 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.308 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.08 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20526 3156 5.1 %RANDOM
Rwork0.16828 ---
all0.17017 59077 --
obs0.17017 59077 98.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.509 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2---0.1 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.48→37.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2588 0 26 431 3045
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222733
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5451.963703
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1425324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.37324.702151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.46415519
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.6961515
X-RAY DIFFRACTIONr_chiral_restr0.1270.2391
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022073
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2220.21321
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.21880
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2308
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2520.277
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2410.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7251.51620
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.44322513
X-RAY DIFFRACTIONr_scbond_it3.7131329
X-RAY DIFFRACTIONr_scangle_it4.7794.51179
X-RAY DIFFRACTIONr_rigid_bond_restr2.30132949
X-RAY DIFFRACTIONr_sphericity_free6.8533435
X-RAY DIFFRACTIONr_sphericity_bonded5.87932672
LS refinement shellResolution: 1.478→1.516 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 239 -
Rwork0.203 4033 -
obs-4272 94.14 %

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