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- PDB-3f5b: The crystal structure of aminoglycoside N(6')acetyltransferase fr... -

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Basic information

Entry
Database: PDB / ID: 3f5b
TitleThe crystal structure of aminoglycoside N(6')acetyltransferase from Legionella pneumophila subsp. pneumophila str. Philadelphia 1.
ComponentsAminoglycoside N(6')acetyltransferase
KeywordsTRANSFERASE / APC60744 / aminoglycoside N(6')acetyltransferase / Legionella pneumophila subsp. pneumophila / structural genomics / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG str. Philadelphia 1
Function / homology
Function and homology information


N-acetyltransferase activity
Similarity search - Function
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
ACETATE ION / CYCLOHEXANE / FORMIC ACID / PHOSPHATE ION / Aminoglycoside N(6')acetyltransferase
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsTan, K. / Wu, R. / Perez, V. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of aminoglycoside N(6')acetyltransferase from Legionella pneumophila subsp. pneumophila str. Philadelphia 1.
Authors: Tan, K. / Wu, R. / Perez, V. / Jedrzejczak, R. / Joachimiak, A.
History
DepositionNov 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description ...Advisory / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: Aminoglycoside N(6')acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8819
Polymers21,3971
Non-polymers4848
Water1,62190
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.504, 77.504, 73.178
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsExperimentally unknown. It is predicted to be a monomer.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Aminoglycoside N(6')acetyltransferase


Mass: 21396.748 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria)
Strain: str. Philadelphia 1
Gene: aacA4, Legionella pneumophila subsp. pneumophila, lpg0979
Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q5ZWV6

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Non-polymers , 6 types, 98 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-CHX / CYCLOHEXANE / Cyclohexane


Mass: 84.159 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12
#5: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.57 Å3/Da / Density % sol: 52.1 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 0.056M sodium dihydrogen phosphate, 1.344M di-sodium, hydrogen phosphate, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97926 Å
DetectorType: SBC-3 / Detector: CCD / Date: Jun 26, 2008 / Details: Mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2→54.8 Å / Num. all: 14948 / Num. obs: 14948 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 29
Reflection shellResolution: 2→2.03 Å / Redundancy: 6 % / Rmerge(I) obs: 0.644 / Mean I/σ(I) obs: 2.88 / Num. unique all: 732 / % possible all: 95.7

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
RESOLVEmodel building
HKL-3000phasing
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2→54.8 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.935 / SU B: 7.958 / SU ML: 0.104 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.2 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24399 736 5 %RANDOM
Rwork0.21241 ---
all0.21391 13949 --
obs0.21391 13949 93.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.225 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å20 Å2
2--0.44 Å20 Å2
3----0.88 Å2
Refinement stepCycle: LAST / Resolution: 2→54.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1423 0 31 90 1544
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221514
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.9432043
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1135178
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.65924.7374
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.64815267
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.708154
X-RAY DIFFRACTIONr_chiral_restr0.1070.2214
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211136
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2312882
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.06131418
X-RAY DIFFRACTIONr_scbond_it1.4932632
X-RAY DIFFRACTIONr_scangle_it2.0933620
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.999→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 60 -
Rwork0.249 1025 -
obs-1085 96.44 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5716-1.7668-0.56555.60521.55420.82210.0230.0404-0.0096-0.0446-0.092-0.0201-0.05-0.07830.0690.05210.0208-0.00460.0517-0.00690.043111.927351.07894.8147
21.1339-0.0117-0.3171.5827-0.24861.98530.01640.0095-0.0408-0.0058-0.00810.11-0.0227-0.0657-0.00830.00050.0008-0.0010.0023-0.00080.009130.150922.54513.029
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 2
2X-RAY DIFFRACTION2A9 - 176

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