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- PDB-6mb8: Apo structure of AAC-IIIb -

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Basic information

Entry
Database: PDB / ID: 6mb8
TitleApo structure of AAC-IIIb
ComponentsAac(3)-IIIb protein
KeywordsTRANSFERASE/ANTIBIOTIC / acetyltransferase / promiscuity / GNAT / antibiotic resistance / ANTIBIOTIC / TRANSFERASE-ANTIBIOTIC complex
Function / homologyaminoglycoside 3-N-acetyltransferase activity / Aminoglycoside N(3)-acetyltransferase / Aminoglycoside 3-N-acetyltransferase / Aminoglycoside 3-N-acetyltransferase-like / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / response to antibiotic / Aminoglycoside N(3)-acetyltransferase
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsCuneo, M.J. / Kumar, P.
CitationJournal: J. Med. Chem. / Year: 2018
Title: Encoding of Promiscuity in an Aminoglycoside Acetyltransferase.
Authors: Kumar, P. / Selvaraj, B. / Serpersu, E.H. / Cuneo, M.J.
History
DepositionAug 29, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aac(3)-IIIb protein
B: Aac(3)-IIIb protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1094
Polymers58,0382
Non-polymers712
Water16,159897
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-31 kcal/mol
Surface area21330 Å2
MethodPISA
2
A: Aac(3)-IIIb protein
B: Aac(3)-IIIb protein
hetero molecules

A: Aac(3)-IIIb protein
B: Aac(3)-IIIb protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,2178
Polymers116,0754
Non-polymers1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area7590 Å2
ΔGint-76 kcal/mol
Surface area40720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.256, 163.897, 95.126
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-814-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 7 through 52 or resid 54...
21(chain B and (resid 7 through 52 or resid 54...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERLEULEU(chain A and (resid 7 through 52 or resid 54...AA7 - 527 - 52
12ASPASPGLYGLY(chain A and (resid 7 through 52 or resid 54...AA54 - 10554 - 105
13SERSERTHRTHR(chain A and (resid 7 through 52 or resid 54...AA7 - 2717 - 271
14SERSERTHRTHR(chain A and (resid 7 through 52 or resid 54...AA7 - 2717 - 271
15ILEILEARGARG(chain A and (resid 7 through 52 or resid 54...AA190 - 206190 - 206
16ILEILEPHEPHE(chain A and (resid 7 through 52 or resid 54...AA208 - 211208 - 211
17THRTHRGLYGLY(chain A and (resid 7 through 52 or resid 54...AA213 - 270213 - 270
21SERSERLEULEU(chain B and (resid 7 through 52 or resid 54...BB7 - 527 - 52
22ASPASPGLYGLY(chain B and (resid 7 through 52 or resid 54...BB54 - 10554 - 105
23ALAALAGLYGLY(chain B and (resid 7 through 52 or resid 54...BB6 - 2706 - 270
24ALAALAGLYGLY(chain B and (resid 7 through 52 or resid 54...BB6 - 2706 - 270
25ILEILEARGARG(chain B and (resid 7 through 52 or resid 54...BB190 - 206190 - 206
26ILEILEPHEPHE(chain B and (resid 7 through 52 or resid 54...BB208 - 211208 - 211
27THRTHRGLYGLY(chain B and (resid 7 through 52 or resid 54...BB213 - 270213 - 270

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Components

#1: Protein Aac(3)-IIIb protein


Mass: 29018.799 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: aac(3)-IIIb / Production host: Escherichia coli DH1 (bacteria) / Strain (production host): DH1 / References: UniProt: Q51405
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 897 / Source method: isolated from a natural source / Formula: H2O
Sequence detailssee NCBI Reference Sequence: WP_088170001.1

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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: 4.61 Å3/Da / Density % sol: 73.31 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / Details: 3.0 M sodium formate, 10-20 % glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→40 Å / Num. obs: 140647 / % possible obs: 99.9 % / Redundancy: 4.1 % / Biso Wilson estimate: 23.08 Å2 / Rmerge(I) obs: 0.038 / Χ2: 1.198 / Net I/σ(I): 21.6 / Num. measured all: 575060
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.6-1.663.90.66139491.523199.9
1.66-1.7240.519139871.5061100
1.72-1.840.361139221.4691100
1.8-1.94.10.242139881.3661100
1.9-2.024.10.153140171.1951100
2.02-2.174.10.096139871.1561100
2.17-2.394.20.062140591.1071100
2.39-2.744.20.043140810.9271100
2.74-3.454.20.026141691.018199.9
3.45-404.20.016144880.806199.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BC3

6bc3


Resolution: 1.6→39.985 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.44
RfactorNum. reflection% reflection
Rfree0.192 1999 1.42 %
Rwork0.179 --
obs0.1792 140555 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 97.69 Å2 / Biso mean: 28.5909 Å2 / Biso min: 13.85 Å2
Refinement stepCycle: final / Resolution: 1.6→39.985 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3976 0 2 897 4875
Biso mean--54.11 40.9 -
Num. residues----530
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1542X-RAY DIFFRACTION4.105TORSIONAL
12B1542X-RAY DIFFRACTION4.105TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.640.26751420.27029828997099
1.64-1.68430.27081410.259997819922100
1.6843-1.73390.29351410.258798319972100
1.7339-1.78980.25761430.239698449987100
1.7898-1.85380.24751420.216998209962100
1.8538-1.9280.24371420.2059985910001100
1.928-2.01580.18791420.1982987410016100
2.0158-2.12210.21631420.190198239965100
2.1221-2.2550.20311420.1833989510037100
2.255-2.42910.20231440.1832989410038100
2.4291-2.67350.19811430.1838989610039100
2.6735-3.06020.20031430.1857995410097100
3.0602-3.85510.16741430.1517997910122100
3.8551-39.99760.1511490.15121027810427100

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