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- PDB-4wqk: Crystal structure of aminoglycoside nucleotidylyltransferase ANT(... -

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Basic information

Entry
Database: PDB / ID: 4wqk
TitleCrystal structure of aminoglycoside nucleotidylyltransferase ANT(2")-Ia, apo form
Components2''-aminoglycoside nucleotidyltransferase
KeywordsTRANSFERASE / antibiotic resistance / aminoglycosides / kanamycin / nucleotidylyltransferase / adenylyltransferase / nucleotidyltransferase fold / alpha/beta protein / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID / National Institute of Allergy and Infectious Diseases / NIAID
Function / homology
Function and homology information


gentamicin 2''-nucleotidyltransferase / aminoglycoside 2''-nucleotidyltransferase activity / response to antibiotic / metal ion binding
Similarity search - Function
Aminoglycoside-2''-adenylyltransferase / Aminoglycoside-2''-adenylyltransferase / Beta Polymerase; domain 2 - #40 / Beta Polymerase; domain 2 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / 2''-aminoglycoside nucleotidyltransferase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.482 Å
AuthorsCox, G. / Stogios, P.J. / Savchenko, A. / Wright, G.D. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support Canada, 2items
OrganizationGrant numberCountry
Canada Foundation for Innovation26332 Canada
Canadian Institutes of Health Research (CIHR)MT-13536 Canada
CitationJournal: Mbio / Year: 2015
Title: Structural and Molecular Basis for Resistance to Aminoglycoside Antibiotics by the Adenylyltransferase ANT(2)-Ia.
Authors: Cox, G. / Stogios, P.J. / Savchenko, A. / Wright, G.D.
History
DepositionOct 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Other
Revision 1.2Jan 28, 2015Group: Database references
Revision 1.3Feb 22, 2017Group: Structure summary
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2''-aminoglycoside nucleotidyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,72814
Polymers19,9501
Non-polymers77713
Water4,720262
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-19 kcal/mol
Surface area9330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.528, 42.110, 47.702
Angle α, β, γ (deg.)90.00, 105.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 2''-aminoglycoside nucleotidyltransferase / AAD(2'') / Gentamicin 2''-nucleotidyltransferase / Gentamicin resistance protein


Mass: 19950.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: aadB / Plasmid: pDEST15 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta
References: UniProt: P0AE05, gentamicin 2''-nucleotidyltransferase

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Non-polymers , 5 types, 275 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 60 mg/mL protein, 10% 2-propanol, 20% PEG4K, 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.48→40 Å / Num. obs: 28211 / % possible obs: 96.8 % / Redundancy: 7 % / Biso Wilson estimate: 18.94 Å2 / Rsym value: 0.036 / Net I/σ(I): 63.68
Reflection shellResolution: 1.48→1.51 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 5.39 / % possible all: 77.4

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Processing

Software
NameVersionClassification
HKL-3000data reduction
HKL-3000data scaling
PHENIXphenix.autosolphasing
PHENIXmodel building
Cootmodel building
PHENIX(phenix.refine: 1.9_1692)refinement
RefinementMethod to determine structure: SAD / Resolution: 1.482→37.066 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1959 1995 7.11 %Random selection
Rwork0.1587 ---
obs0.1613 28068 96.29 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.52 Å2
Refinement stepCycle: LAST / Resolution: 1.482→37.066 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1385 0 48 262 1695
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121493
X-RAY DIFFRACTIONf_angle_d1.4412033
X-RAY DIFFRACTIONf_dihedral_angle_d12.91547
X-RAY DIFFRACTIONf_chiral_restr0.067213
X-RAY DIFFRACTIONf_plane_restr0.008263
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4816-1.51860.32061180.28341517X-RAY DIFFRACTION78
1.5186-1.55970.24171250.19931789X-RAY DIFFRACTION93
1.5597-1.60560.23081430.17181807X-RAY DIFFRACTION95
1.6056-1.65740.20421360.16081823X-RAY DIFFRACTION96
1.6574-1.71670.18251380.16221892X-RAY DIFFRACTION97
1.7167-1.78540.22321490.16581847X-RAY DIFFRACTION97
1.7854-1.86660.21261450.16411870X-RAY DIFFRACTION98
1.8666-1.96510.23361400.16181886X-RAY DIFFRACTION98
1.9651-2.08820.21121440.15551911X-RAY DIFFRACTION99
2.0882-2.24940.20621500.15671920X-RAY DIFFRACTION99
2.2494-2.47570.20581510.16351925X-RAY DIFFRACTION100
2.4757-2.83380.19361520.15471943X-RAY DIFFRACTION100
2.8338-3.56990.18121490.1431945X-RAY DIFFRACTION100
3.5699-37.07770.16871550.15851998X-RAY DIFFRACTION100
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)
12.2761-0.5599-0.86624.03530.33523.09520.0555-0.02940.16840.10490.0134-0.1429-0.15450.1135-0.07360.0734-0.0056-0.00780.10180.01350.10198.174424.15376.523
25.1844-0.2805-0.10178.7151-4.80718.39060.1107-0.2733-0.24010.214-0.1808-0.63160.17970.63880.0850.09780.0033-0.04720.2250.01740.240519.751419.00849.2763
30.36280.0085-0.14121.70170.0211.45460.0229-0.00940.01580.1247-0.0318-0.01480.0755-0.04670.0150.1422-0.00670.00390.14780.00330.14451.913718.252412.9627
48.14582.97732.48655.9302-2.61573.34460.1708-0.1223-0.15490.4857-0.2683-0.65520.06950.39220.14220.29540.0059-0.07020.2483-0.0610.29787.345127.003229.1957
54.6681-2.0059-0.60453.2324-2.12792.8419-0.0679-0.2185-0.22930.66440.14390.3348-0.2258-0.0668-0.04720.194-0.0321-0.01150.1827-0.0190.1268-4.587619.099127.3352
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 3:61)
2X-RAY DIFFRACTION2(chain A and resid 62:82)
3X-RAY DIFFRACTION3(chain A and resid 83:136)
4X-RAY DIFFRACTION4(chain A and resid 137:152)
5X-RAY DIFFRACTION5(chain A and resid 153:177)

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