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- PDB-3fbu: The crystal structure of the acetyltransferase (GNAT family) from... -

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Basic information

Entry
Database: PDB / ID: 3fbu
TitleThe crystal structure of the acetyltransferase (GNAT family) from Bacillus anthracis
ComponentsAcetyltransferase, GNAT family
KeywordsTRANSFERASE / acetyltransferase (GNAT family) / Bacillus anthracis / structural genomics / PSI2 / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


N-acetyltransferase activity / transferase activity
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
COENZYME A / Acetyltransferase, GNAT family / Acetyltransferase, GNAT family
Similarity search - Component
Biological speciesBacillus anthracis str. Sterne (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsZhang, R. / Xu, X. / Cui, H. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the acetyltransferase (GNAT family) from Bacillus anthracis
Authors: Zhang, R. / Xu, X. / Cui, H. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionNov 19, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2May 6, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_gen.assembly_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.biol_id
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Acetyltransferase, GNAT family
B: Acetyltransferase, GNAT family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9533
Polymers40,1862
Non-polymers7681
Water3,261181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Acetyltransferase, GNAT family
hetero molecules

B: Acetyltransferase, GNAT family


Theoretical massNumber of molelcules
Total (without water)40,9533
Polymers40,1862
Non-polymers7681
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_664-x+3/2,-y+1,z-1/21
Buried area2730 Å2
ΔGint-9 kcal/mol
Surface area17100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.421, 84.275, 97.755
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThis protein existed as dimer. The deposited MolA and MolB represent the dimer in the asymmetric unit.

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Components

#1: Protein Acetyltransferase, GNAT family /


Mass: 20092.881 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis str. Sterne (bacteria)
Strain: str. Sterne] / Gene: BAS2358, BA_2534, GBAA2534, GI:49185367 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q81Q99, UniProt: A0A6L8PM89*PLUS
#2: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.12 Å3/Da / Density % sol: 42.06 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1M Mes, 10% PEG10000, 1mM ACoA, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 24, 2008 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.8→63.89 Å / Num. all: 30854 / Num. obs: 30700 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.9 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 27.56
Reflection shellResolution: 1.8→1.847 Å / Redundancy: 5 % / Rmerge(I) obs: 0.743 / Mean I/σ(I) obs: 1.89 / Num. unique all: 2350 / % possible all: 96

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
REFMAC5.2.0019refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.8→63.89 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.348 / SU ML: 0.083 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.147 / ESU R Free: 0.129
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22352 1643 5.1 %RANDOM
Rwork0.19818 ---
obs0.19954 30700 99.5 %-
all-30854 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.648 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20 Å2
2--0.24 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.8→63.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2806 0 48 181 3035
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222940
X-RAY DIFFRACTIONr_bond_other_d0.0010.022040
X-RAY DIFFRACTIONr_angle_refined_deg1.4951.9483967
X-RAY DIFFRACTIONr_angle_other_deg0.89434924
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1465328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.62823.806155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.36315507
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6981514
X-RAY DIFFRACTIONr_chiral_restr0.0940.2387
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023199
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02652
X-RAY DIFFRACTIONr_nbd_refined0.2060.2509
X-RAY DIFFRACTIONr_nbd_other0.190.22003
X-RAY DIFFRACTIONr_nbtor_refined0.190.21386
X-RAY DIFFRACTIONr_nbtor_other0.0860.21465
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2116
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1530.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2810.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1020.215
X-RAY DIFFRACTIONr_mcbond_it1.4911.52150
X-RAY DIFFRACTIONr_mcbond_other0.2491.5671
X-RAY DIFFRACTIONr_mcangle_it1.61322657
X-RAY DIFFRACTIONr_scbond_it2.77631585
X-RAY DIFFRACTIONr_scangle_it3.5124.51310
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 100 -
Rwork0.221 2156 -
obs-2256 96 %
Refinement TLS params.Method: refined / Origin x: 32.813 Å / Origin y: 56.791 Å / Origin z: 29.742 Å
111213212223313233
T-0.0142 Å20.0002 Å20.0087 Å2--0.0128 Å2-0.0035 Å2--0.0043 Å2
L0.3326 °2-0.0987 °20.3337 °2-0.0362 °2-0.1461 °2--0.6533 °2
S-0.0035 Å °-0.0098 Å °-0.0637 Å °-0.0014 Å °0.0108 Å °-0.0149 Å °-0.0747 Å °-0.003 Å °-0.0072 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 168
2X-RAY DIFFRACTION1B1 - 168
3X-RAY DIFFRACTION1A169

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