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- PDB-6nmn: Ternary complex structure of the T130K mutant of ANT-4'' with Neo... -

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Basic information

Entry
Database: PDB / ID: 6nmn
TitleTernary complex structure of the T130K mutant of ANT-4'' with Neomycin and ATP (No Pyrophosphate)
ComponentsKanamycin nucleotidyltransferase
Keywordstransferase/ANTIBIOTIC / Aminoglycoside nucelotidyl transferase (ANT) Aminoglycoside modifying enzymes (AGMEs) DNA polymerase / ANTIBIOTIC / transferase-ANTIBIOTIC complex
Function / homology
Function and homology information


nucleotidyltransferase activity / response to antibiotic / metal ion binding
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
ADENOSINE MONOPHOSPHATE / NEOMYCIN / Kanamycin nucleotidyltransferase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsCuneo, M.J. / Selvaraj, B.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
Department of Energy (DOE, United States) United States
CitationJournal: to be published
Title: Catch and release: A novel variation of the archetypal nucleotidyl transfer reaction
Authors: Selvaraj, B. / Cuneo, M.J.
History
DepositionJan 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Database references / Category: citation_author
Revision 1.2Feb 26, 2020Group: Database references / Category: citation_author
Revision 1.3Mar 13, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type
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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 2.0May 29, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.auth_comp_id ..._atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _chem_comp_atom.atom_id / _chem_comp_atom.comp_id / _chem_comp_atom.pdbx_aromatic_flag / _chem_comp_atom.pdbx_stereo_config / _chem_comp_atom.type_symbol / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.comp_id / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kanamycin nucleotidyltransferase
B: Kanamycin nucleotidyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2689
Polymers58,2722
Non-polymers1,9977
Water9,134507
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8630 Å2
ΔGint-63 kcal/mol
Surface area20370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.050, 58.050, 363.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-1134-

HOH

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Components

#1: Protein Kanamycin nucleotidyltransferase /


Mass: 29135.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: Q57514
#2: Chemical ChemComp-NMY / NEOMYCIN / MYCIFRADIN / NEOMAS / PIMAVECORT / VONAMYCIN / Neomycin


Mass: 614.644 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H46N6O13 / Comment: antibiotic*YM
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 507 / 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: 2.63 Å3/Da / Density % sol: 53.18 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop
Details: crystallized in 9-10% PEG 5K MME, 0.1 M Tris pH 7.5-8.0, 0.1-0.2 M CaCl2. The crystals were transferred to a cryosolution containing 9-10% PEG 5K MME, 0.1 M Tris pH 7.5-8.0, 10 mM MgCl2 and ...Details: crystallized in 9-10% PEG 5K MME, 0.1 M Tris pH 7.5-8.0, 0.1-0.2 M CaCl2. The crystals were transferred to a cryosolution containing 9-10% PEG 5K MME, 0.1 M Tris pH 7.5-8.0, 10 mM MgCl2 and 30% glycerol for varying time intervals (3-30 min)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.8→60.57 Å / Num. obs: 54803 / % possible obs: 92.1 % / Redundancy: 5.3 % / CC1/2: 0.994 / Rmerge(I) obs: 0.76 / Rpim(I) all: 0.034 / Rrim(I) all: 0.084 / Net I/σ(I): 12.2
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 5 / Num. unique obs: 2770 / CC1/2: 0.945 / Rpim(I) all: 0.102 / Rrim(I) all: 0.27 / % possible all: 80.7

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-3000data reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.8→57.323 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.38
RfactorNum. reflection% reflection
Rfree0.2182 2812 5.14 %
Rwork0.1845 --
obs0.1862 54657 91.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→57.323 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4054 0 131 507 4692
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054456
X-RAY DIFFRACTIONf_angle_d0.7766080
X-RAY DIFFRACTIONf_dihedral_angle_d4.0823517
X-RAY DIFFRACTIONf_chiral_restr0.047677
X-RAY DIFFRACTIONf_plane_restr0.004769
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.83110.30381120.24812203X-RAY DIFFRACTION80
1.8311-1.86440.27131310.25132271X-RAY DIFFRACTION82
1.8644-1.90020.31081100.23312280X-RAY DIFFRACTION83
1.9002-1.9390.2651300.22052335X-RAY DIFFRACTION84
1.939-1.98120.27341350.20342340X-RAY DIFFRACTION87
1.9812-2.02730.24591430.21452374X-RAY DIFFRACTION85
2.0273-2.0780.23931420.20562439X-RAY DIFFRACTION88
2.078-2.13420.26591360.20322476X-RAY DIFFRACTION89
2.1342-2.1970.22211440.19762440X-RAY DIFFRACTION89
2.197-2.26790.24961450.19472574X-RAY DIFFRACTION92
2.2679-2.34890.21911490.19072588X-RAY DIFFRACTION92
2.3489-2.4430.23271350.19212687X-RAY DIFFRACTION96
2.443-2.55420.2341470.192714X-RAY DIFFRACTION97
2.5542-2.68880.21981390.19132757X-RAY DIFFRACTION98
2.6888-2.85730.21791480.18972778X-RAY DIFFRACTION98
2.8573-3.07790.20521520.19452816X-RAY DIFFRACTION98
3.0779-3.38760.23351360.17752838X-RAY DIFFRACTION99
3.3876-3.87770.19181490.16732884X-RAY DIFFRACTION99
3.8777-4.88510.17631470.14852931X-RAY DIFFRACTION99
4.8851-57.35250.19891820.17753120X-RAY DIFFRACTION99

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