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- PDB-6bbz: Room temperature neutron/X-ray structure of sisomicin bound AAC-VIa -

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Basic information

Entry
Database: PDB / ID: 6bbz
TitleRoom temperature neutron/X-ray structure of sisomicin bound AAC-VIa
ComponentsAAC 3-VI protein
KeywordsTRANSFERASE/ANTIBIOTIC / acetyltransferase / TRANSFERASE-ANTIBIOTIC complex
Function / homologyaminoglycoside 3-N-acetyltransferase / aminoglycoside 3-N-acetyltransferase activity / Aminoglycoside N(3)-acetyltransferase / Aminoglycoside 3-N-acetyltransferase / Aminoglycoside 3-N-acetyltransferase-like / response to antibiotic / metal ion binding / Chem-SIS / Aminoglycoside N(3)-acetyltransferase
Function and homology information
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCuneo, M.J. / Kumar, P.
CitationJournal: Sci Adv / Year: 2018
Title: A low-barrier hydrogen bond mediates antibiotic resistance in a noncanonical catalytic triad.
Authors: Kumar, P. / Serpersu, E.H. / Cuneo, M.J.
History
DepositionOct 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.2Sep 12, 2018Group: Data collection / 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Oct 4, 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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: AAC 3-VI protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8163
Polymers32,3441
Non-polymers4722
Water2,270126
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-6 kcal/mol
Surface area11880 Å2
Unit cell
Length a, b, c (Å)50.822, 86.169, 76.900
Angle α, β, γ (deg.)90.00, 94.55, 90.00
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-302-

MG

21A-517-

HOH

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Components

#1: Protein AAC 3-VI protein / AAC-VIa


Mass: 32344.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: aac 3-VI / Production host: Escherichia coli (E. coli) / References: UniProt: Q47030
#2: Chemical ChemComp-SIS / (1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2S,3R)-3-amino-6-(aminomethyl)-3,4-dihydro-2H-pyran-2-yl]oxy}-2-hydroxycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside / Sisomicin / Sisomicin


Mass: 447.526 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H37N5O7 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION1

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris, pH 8.5, 0.3 M magnesium chloride, 15-17% PEG8000

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12981
22981
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU MICROMAX-007 HF11.5418
NUCLEAR REACTORORNL Spallation Neutron Source MANDI22.0-4.0
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV++1IMAGE PLATEJul 1, 2017
ORNL ANGER CAMERA2DIFFRACTOMETERJul 1, 2017
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2LAUELneutron2
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
221
341
Reflection

Biso Wilson estimate: 32.2 Å2 / Entry-ID: 6BBZ

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)CC1/2Rmerge(I) obsRpim(I) allRrim(I) allDiffraction-IDNet I/σ(I)
1.9-502587499.251.660.9970.0470.0470.067117.2
2.2-15.571586092.23.40.9790.1480.0870.173210.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.972.10.40125250.8390.3130.5111.59497.2
1.97-2.052.40.32125790.8860.2460.4061.66199.5
2.05-2.142.40.24326000.9260.1850.3071.84199.5
2.14-2.252.40.16525450.9630.1250.2081.94499.3
2.25-2.392.40.12726110.9780.0970.1612.21199.4
2.39-2.582.40.08925870.9890.0670.1122.13599.4
2.58-2.842.40.06525680.9920.0490.0812.34399.4
2.84-3.252.40.04526030.9960.0330.0562.29599.6
3.25-4.092.50.03126070.9980.0230.0382.09999.5
4.09-502.40.03126240.9970.0230.0382.33798.6

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Processing

Software
NameVersionClassification
PHENIX(1.11_2567: ???)refinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
PHASERphasing
Refinement

Method to determine structure: MOLECULAR REPLACEMENT / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Starting model: PDB entry 6BC6

6bc6

/ Stereochemistry target values: ML / Solvent model: FLAT BULK SOLVENT MODEL

Resolution (Å)Refine-IDRfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection obs% reflection Rfree (%)% reflection obs (%)SU MLCross valid methodσ(F)Phase error
1.9-38.329X-RAY DIFFRACTION0.18140.15030.15191286258674.9799.230.19FREE R-VALUE1.3420.2
2.2-15.433NEUTRON DIFFRACTION0.21990.19760.1987763155124.9292.470.3629.99
Refinement stepCycle: LAST / Resolution: 1.9→38.329 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2023 0 32 126 2181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134776
X-RAY DIFFRACTIONf_angle_d0.818351
X-RAY DIFFRACTIONf_dihedral_angle_d19.4761240
X-RAY DIFFRACTIONf_chiral_restr0.074317
X-RAY DIFFRACTIONf_plane_restr0.004919
NEUTRON DIFFRACTIONf_bond_d0.0134776
NEUTRON DIFFRACTIONf_angle_d0.818351
NEUTRON DIFFRACTIONf_dihedral_angle_d19.4761240
NEUTRON DIFFRACTIONf_chiral_restr0.074317
NEUTRON DIFFRACTIONf_plane_restr0.004919
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.97610.26691410.23672661X-RAY DIFFRACTION97
1.9761-2.0660.26161470.21122729X-RAY DIFFRACTION100
2.066-2.17490.21591390.18542725X-RAY DIFFRACTION99
2.1749-2.31120.19941440.172737X-RAY DIFFRACTION99
2.3112-2.48960.23331380.1672727X-RAY DIFFRACTION100
2.4896-2.74010.18871500.16582724X-RAY DIFFRACTION100
2.7401-3.13640.20021350.17682753X-RAY DIFFRACTION100
3.1364-3.95090.17121460.14012752X-RAY DIFFRACTION100
3.9509-38.33640.1431460.1132773X-RAY DIFFRACTION99
2.2001-2.36940.36561490.35962856NEUTRON DIFFRACTION90
2.3694-2.60680.32461440.3072887NEUTRON DIFFRACTION91
2.6068-2.98170.26491540.25573002NEUTRON DIFFRACTION94
2.9817-3.74770.22061590.20393049NEUTRON DIFFRACTION96
3.7477-15.43310.17061570.13792955NEUTRON DIFFRACTION92

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