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- PDB-6p01: Apo structure of the E52D mutant of ANT-4 -

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Basic information

Entry
Database: PDB / ID: 6p01
TitleApo structure of the E52D mutant of ANT-4
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 / 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
Aminoglycoside nucleotidyltransferase (4')
Similarity search - Component
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsSelvaraj, B. / Cuneo, M.J.
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
DepositionMay 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation
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.year
Revision 1.2May 20, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Oct 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 / _struct_conn.ptnr2_label_seq_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)58,67510
Polymers58,2442
Non-polymers4318
Water6,557364
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7230 Å2
ΔGint-88 kcal/mol
Surface area20810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.340, 97.040, 100.850
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: 29121.855 Da / Num. of mol.: 2 / Mutation: E52D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. (bacteria) / Gene: knt, kan
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: P05058, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / 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: 2.37 Å3/Da / Density % sol: 48.03 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop
Details: 16-18% PEG 8K, 0.1 M Tris pH 7.5-8.0, 0.1-0.2 M MgCl2.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.89→49.19 Å / Num. obs: 45256 / % possible obs: 99.9 % / Redundancy: 6.1 % / Biso Wilson estimate: 13.1 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.054 / Rrim(I) all: 0.135 / Net I/σ(I): 10.6
Reflection shellResolution: 1.89→1.93 Å / Redundancy: 6 % / Rmerge(I) obs: 0.634 / Mean I/σ(I) obs: 3 / Num. unique obs: 2873 / CC1/2: 0.793 / Rpim(I) all: 0.281 / Rrim(I) all: 0.695 / Χ2: 0.69 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KNY

1kny


Resolution: 1.89→49.185 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.1
RfactorNum. reflection% reflection
Rfree0.2061 2207 4.88 %
Rwork0.1756 --
obs0.1772 45191 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.89→49.185 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4036 0 23 364 4423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084259
X-RAY DIFFRACTIONf_angle_d1.1475786
X-RAY DIFFRACTIONf_dihedral_angle_d8.1523457
X-RAY DIFFRACTIONf_chiral_restr0.056625
X-RAY DIFFRACTIONf_plane_restr0.007746
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.9280.27481410.22892635X-RAY DIFFRACTION100
1.928-1.97290.24631220.20952647X-RAY DIFFRACTION100
1.9729-2.02220.26011470.21022659X-RAY DIFFRACTION100
2.0222-2.07690.26211410.20122634X-RAY DIFFRACTION100
2.0769-2.1380.25611320.19512646X-RAY DIFFRACTION100
2.138-2.2070.22171430.17942653X-RAY DIFFRACTION100
2.207-2.28590.22021170.18012701X-RAY DIFFRACTION100
2.2859-2.37740.21221280.1822657X-RAY DIFFRACTION100
2.3774-2.48560.23461310.17692675X-RAY DIFFRACTION100
2.4856-2.61670.23041340.18042669X-RAY DIFFRACTION100
2.6167-2.78060.20341560.18382652X-RAY DIFFRACTION100
2.7806-2.99530.22781370.18062700X-RAY DIFFRACTION100
2.9953-3.29660.22441300.17552723X-RAY DIFFRACTION100
3.2966-3.77350.17751380.15772721X-RAY DIFFRACTION100
3.7735-4.75360.15611750.14012715X-RAY DIFFRACTION100
4.7536-49.20180.17371350.17542897X-RAY DIFFRACTION100

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