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- PDB-6mb6: AAC-IIIb binary with CoASH -

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Basic information

Entry
Database: PDB / ID: 6mb6
TitleAAC-IIIb binary with CoASH
ComponentsAac(3)-IIIb protein
KeywordsTRANSFERASE / acetyltransferase / promiscuity / GNAT / antibiotic resistance
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 / COENZYME A / MALONATE ION / Aminoglycoside N(3)-acetyltransferase
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.25 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 1.2Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)117,8148
Polymers116,0754
Non-polymers1,7394
Water10,809600
1
A: Aac(3)-IIIb protein
C: Aac(3)-IIIb protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5734
Polymers58,0382
Non-polymers1,5352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aac(3)-IIIb protein
D: Aac(3)-IIIb protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2424
Polymers58,0382
Non-polymers2042
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9720 Å2
ΔGint-21 kcal/mol
Surface area41200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.797, 80.741, 103.546
Angle α, β, γ (deg.)90.000, 108.420, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 8 through 55 or resid 57...
21(chain B and (resid 8 through 55 or resid 57...
31(chain C and (resid 8 through 55 or resid 57...
41(chain D and (resid 8 through 55 or resid 57...

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
11PHEPHETHRTHR(chain A and (resid 8 through 55 or resid 57...AA8 - 558 - 55
12GLYGLYPROPRO(chain A and (resid 8 through 55 or resid 57...AA57 - 9557 - 95
13ARGARGLEULEU(chain A and (resid 8 through 55 or resid 57...AA97 - 1497 - 14
14SERSERPROPRO(chain A and (resid 8 through 55 or resid 57...AA7 - 2747 - 274
15GLUGLUARGARG(chain A and (resid 8 through 55 or resid 57...AA194 - 206194 - 206
16ILEILEGLYGLY(chain A and (resid 8 through 55 or resid 57...AA208 - 270208 - 270
21PHEPHETHRTHR(chain B and (resid 8 through 55 or resid 57...BB8 - 558 - 55
22GLYGLYPROPRO(chain B and (resid 8 through 55 or resid 57...BB57 - 9557 - 95
23ARGARGLEULEU(chain B and (resid 8 through 55 or resid 57...BB97 - 1497 - 14
24SERSERGLYGLY(chain B and (resid 8 through 55 or resid 57...BB7 - 2707 - 270
25GLUGLUARGARG(chain B and (resid 8 through 55 or resid 57...BB194 - 206194 - 206
26ILEILEGLYGLY(chain B and (resid 8 through 55 or resid 57...BB208 - 270208 - 270
31PHEPHETHRTHR(chain C and (resid 8 through 55 or resid 57...CC8 - 558 - 55
32GLYGLYPROPRO(chain C and (resid 8 through 55 or resid 57...CC57 - 9557 - 95
33ARGARGLEULEU(chain C and (resid 8 through 55 or resid 57...CC97 - 1497 - 14
34PHEPHEPROPRO(chain C and (resid 8 through 55 or resid 57...CC8 - 2728 - 272
35GLUGLUARGARG(chain C and (resid 8 through 55 or resid 57...CC194 - 206194 - 206
36ILEILEGLYGLY(chain C and (resid 8 through 55 or resid 57...CC208 - 270208 - 270
41PHEPHETHRTHR(chain D and (resid 8 through 55 or resid 57...DD8 - 558 - 55
42GLYGLYPROPRO(chain D and (resid 8 through 55 or resid 57...DD57 - 9557 - 95
43ARGARGLEULEU(chain D and (resid 8 through 55 or resid 57...DD97 - 1497 - 14
44SERSERGLYGLY(chain D and (resid 8 through 55 or resid 57...DD7 - 2707 - 270
45GLUGLUARGARG(chain D and (resid 8 through 55 or resid 57...DD194 - 206194 - 206
46ILEILEGLYGLY(chain D and (resid 8 through 55 or resid 57...DD208 - 270208 - 270

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Components

#1: Protein
Aac(3)-IIIb protein


Mass: 29018.799 Da / Num. of mol.: 4
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-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 600 / 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: 2.86 Å3/Da / Density % sol: 57.04 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7.6 / Details: 3.0M 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: 1.54 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: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.25→40 Å / Num. obs: 58550 / % possible obs: 93.7 % / Redundancy: 2.9 % / Biso Wilson estimate: 30.68 Å2 / Rmerge(I) obs: 0.099 / Χ2: 1.487 / Net I/σ(I): 10.6 / Num. measured all: 167223
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.25-2.332.60.67156231.894190.6
2.33-2.422.70.52857521.645192.5
2.42-2.532.70.44357261.657192.1
2.53-2.672.70.33857191.676192.4
2.67-2.832.80.27257511.676192.3
2.83-3.052.90.1858111.628193
3.05-3.3630.10559191.436194.8
3.36-3.852.90.07359821.541195.9
3.85-4.843.10.04961351.149197.6
4.84-103.10.03661320.885195.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
PHASERphasing
RefinementResolution: 2.25→39.753 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.95
RfactorNum. reflection% reflection
Rfree0.2462 2886 4.93 %
Rwork0.2061 --
obs0.208 58526 93.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.34 Å2 / Biso mean: 36.7542 Å2 / Biso min: 14.59 Å2
Refinement stepCycle: final / Resolution: 2.25→39.753 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7967 0 110 600 8677
Biso mean--49.88 36.54 -
Num. residues----1061
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4649X-RAY DIFFRACTION11.294TORSIONAL
12B4649X-RAY DIFFRACTION11.294TORSIONAL
13C4649X-RAY DIFFRACTION11.294TORSIONAL
14D4649X-RAY DIFFRACTION11.294TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.25-2.28450.44361190.42238785
2.2845-2.32390.33341390.3036260992
2.3239-2.36610.311380.2836257592
2.3661-2.41160.32311370.2784260992
2.4116-2.46090.27751330.2664261792
2.4609-2.51440.3311370.2623256792
2.5144-2.57280.2821420.2527261793
2.5728-2.63720.30191310.2528261592
2.6372-2.70850.3241330.2608257591
2.7085-2.78810.30881170.2595262392
2.7881-2.87810.30641410.2412260293
2.8781-2.98090.27061420.2367264093
2.9809-3.10020.25141390.2244264194
3.1002-3.24130.24531270.2062269095
3.2413-3.41210.26451520.2002269296
3.4121-3.62570.23331510.186274797
3.6257-3.90540.23031210.1848270895
3.9054-4.2980.20371360.1601279898
4.298-4.9190.17361530.1423278998
4.919-6.19360.21161590.1607275797
6.1936-39.7530.17231390.1665278295

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