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- PDB-6un8: Wild type ANT bound to neomycin -

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Basic information

Entry
Database: PDB / ID: 6un8
TitleWild type ANT bound to neomycin
ComponentsAminoglycoside NucleotidylTransferase
KeywordsTRANSFERASE/ANTIBIOTIC / antibiotic resistance / neomycin / TRANSFERASE-ANTIBIOTIC complex
Function / homology
Function and homology information


nucleotidyltransferase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / response to antibiotic
Similarity search - Function
Kanamycin nucleotidyltransferase, C-terminal / KNTase C-terminal domain / Nucleotidyltransferases domain 2 / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NEOMYCIN / Kanamycin nucleotidyltransferase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsCuneo, M.J. / Selvaraj, B.
CitationJournal: ACS Catal / Year: 2020
Title: "Catch and Release": a Variation of the Archetypal NucleotidylTransfer Reaction
Authors: Selvaraj, B. / Kocaman, S. / Trifas, M. / Serpersu, E.H. / Cuneo, M.J.
History
DepositionOct 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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_initial_refinement_model / pdbx_struct_conn_angle / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminoglycoside NucleotidylTransferase
B: Aminoglycoside NucleotidylTransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9055
Polymers57,6512
Non-polymers1,2543
Water9,008500
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7610 Å2
ΔGint-39 kcal/mol
Surface area21060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.661, 97.794, 102.231
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 38 or resid 40...
21(chain B and (resid 2 through 38 or resid 40...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 2 through 38 or resid 40...A2 - 38
121(chain A and (resid 2 through 38 or resid 40...A40 - 48
131(chain A and (resid 2 through 38 or resid 40...A50 - 53
141(chain A and (resid 2 through 38 or resid 40...A56 - 64
151(chain A and (resid 2 through 38 or resid 40...A88 - 93
161(chain A and (resid 2 through 38 or resid 40...A2 - 301
171(chain A and (resid 2 through 38 or resid 40...A2 - 301
181(chain A and (resid 2 through 38 or resid 40...A126 - 137
191(chain A and (resid 2 through 38 or resid 40...A140 - 202
1101(chain A and (resid 2 through 38 or resid 40...A204 - 2258
1111(chain A and (resid 2 through 38 or resid 40...A230 - 28
1121(chain A and (resid 2 through 38 or resid 40...A230 - 253
211(chain B and (resid 2 through 38 or resid 40...B2 - 38
221(chain B and (resid 2 through 38 or resid 40...B40 - 48
231(chain B and (resid 2 through 38 or resid 40...B50 - 53
241(chain B and (resid 2 through 38 or resid 40...B66 - 86
251(chain B and (resid 2 through 38 or resid 40...B88 - 93
261(chain B and (resid 2 through 38 or resid 40...B95 - 104
271(chain B and (resid 2 through 38 or resid 40...B106 - 111
281(chain B and (resid 2 through 38 or resid 40...B113 - 124
291(chain B and (resid 2 through 38 or resid 40...B126 - 137
2101(chain B and (resid 2 through 38 or resid 40...B140 - 202
2111(chain B and (resid 2 through 38 or resid 40...B204 - 225
2121(chain B and (resid 2 through 38 or resid 40...B227 - 228
2131(chain B and (resid 2 through 38 or resid 40...B230 - 253

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Components

#1: Protein Aminoglycoside NucleotidylTransferase / ANT / Kanamycin nucleotidyltransferase


Mass: 28825.525 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: knt, kan / Production host: Escherichia coli K-12 (bacteria)
References: UniProt: P05057, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical ChemComp-NMY / NEOMYCIN / MYCIFRADIN / NEOMAS / PIMAVECORT / VONAMYCIN


Mass: 614.644 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H46N6O13 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 500 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.46 Å3/Da / Density % sol: 49.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 16-17% PEG 8K, 0.1 M Tris pH 7-8, 0.1-0.2 M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.649→50 Å / Num. obs: 68631 / % possible obs: 99.2 % / Redundancy: 4.3 % / Rrim(I) all: 0.061 / Net I/σ(I): 24.2
Reflection shellResolution: 1.649→1.71 Å / Redundancy: 4 % / Num. unique obs: 6808 / CC1/2: 0.931 / Rrim(I) all: 0.615 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
PDB_EXTRACT3.25data extraction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KNY

1kny


Resolution: 1.65→50 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.36
RfactorNum. reflection% reflection
Rfree0.1978 1989 2.9 %
Rwork0.1736 --
obs0.1743 68577 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93.3 Å2 / Biso mean: 27.0829 Å2 / Biso min: 12.96 Å2
Refinement stepCycle: final / Resolution: 1.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4042 0 85 500 4627
Biso mean--31.06 36.99 -
Num. residues----505
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1358X-RAY DIFFRACTION1.714TORSIONAL
12B1358X-RAY DIFFRACTION1.714TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.65-1.68980.27191450.24460297
1.6898-1.73550.26881380.21954733100
1.7355-1.78660.24321460.2084730100
1.7866-1.84430.24211310.20434745100
1.8443-1.91020.23891380.2044768100
1.9102-1.98670.23221470.19084727100
1.9867-2.07710.19761510.19064740100
2.0771-2.18660.22151440.17954769100
2.1866-2.32360.17691400.1827476099
2.3236-2.5030.2111390.1791476999
2.503-2.75490.21891450.1845476999
2.7549-3.15340.20861370.1823481599
3.1534-3.97280.17721460.1527473997
3.9728-49.5580.15951420.1467492296

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