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- PDB-6nmk: Binary complex structure of the T130K mutant of ANT-4'' with Neomycin -

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Basic information

Entry
Database: PDB / ID: 6nmk
TitleBinary complex structure of the T130K mutant of ANT-4'' with Neomycin
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
NEOMYCIN / Kanamycin nucleotidyltransferase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.94 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: Acs Catalysis / Year: 2020
Title: 'Catch and Release": a Variation of the Archetypal Nucleotidyl Transfer Reaction
Authors: Selvaraj, B. / Kocaman, S. / Trifas, M. / Serpersu, E.H. / 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 1.3May 6, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.4Mar 13, 2024Group: 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 / 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 / _struct_conn.ptnr2_symmetry

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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)59,5907
Polymers58,2722
Non-polymers1,3185
Water6,972387
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Dimer at higher concentration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7840 Å2
ΔGint-57 kcal/mol
Surface area20990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.000, 97.710, 101.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 387 / 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: 2.52 Å3/Da / Density % sol: 51.23 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop
Details: 16-17% PEG 8K, 0.1 M Tris pH 7-8, 0.1-0.2 M MgCl2, 2-4 mM Neomycin

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.94→51.07 Å / Num. obs: 45570 / % possible obs: 97 % / Redundancy: 6.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.023 / Rrim(I) all: 0.061 / Net I/σ(I): 18.5
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 6 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 2739 / CC1/2: 0.905 / Rpim(I) all: 0.159 / Rrim(I) all: 0.408 / % possible all: 93.7

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-3000data reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.94→51.068 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.05
RfactorNum. reflection% reflection
Rfree0.2105 2334 5.13 %
Rwork0.1702 --
obs0.1722 45511 96.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.94→51.068 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4046 0 87 387 4520
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124411
X-RAY DIFFRACTIONf_angle_d1.2056020
X-RAY DIFFRACTIONf_dihedral_angle_d5.9243496
X-RAY DIFFRACTIONf_chiral_restr0.069671
X-RAY DIFFRACTIONf_plane_restr0.007769
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.93880.25181400.20422375X-RAY DIFFRACTION93
1.9388-1.9810.23611420.19252402X-RAY DIFFRACTION93
1.981-2.02710.32461180.19552425X-RAY DIFFRACTION93
2.0271-2.07770.25381270.18442495X-RAY DIFFRACTION95
2.0777-2.13390.23561260.18842455X-RAY DIFFRACTION95
2.1339-2.19670.26081370.18372493X-RAY DIFFRACTION95
2.1967-2.26760.22261440.17792471X-RAY DIFFRACTION95
2.2676-2.34870.24041370.17962525X-RAY DIFFRACTION97
2.3487-2.44270.23661350.17732527X-RAY DIFFRACTION97
2.4427-2.55390.22311240.17942579X-RAY DIFFRACTION97
2.5539-2.68850.2341410.18242559X-RAY DIFFRACTION97
2.6885-2.85690.24261220.19412561X-RAY DIFFRACTION98
2.8569-3.07750.20931530.18622605X-RAY DIFFRACTION99
3.0775-3.38720.24281390.17832609X-RAY DIFFRACTION99
3.3872-3.87710.17931510.15122625X-RAY DIFFRACTION99
3.8771-4.88420.1661390.13662697X-RAY DIFFRACTION99
4.8842-51.08620.16781590.16182774X-RAY DIFFRACTION98

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