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- PDB-6mb4: Binary (sisomicin) structure of AAC-IIIb -

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Basic information

Entry
Database: PDB / ID: 6mb4
TitleBinary (sisomicin) 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 / Chem-SIS / Aminoglycoside N(3)-acetyltransferase
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.302 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
C: Aac(3)-IIIb protein
D: Aac(3)-IIIb protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,5235
Polymers116,0754
Non-polymers4481
Water11,331629
1
A: Aac(3)-IIIb protein
B: Aac(3)-IIIb protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4853
Polymers58,0382
Non-polymers4481
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-7 kcal/mol
Surface area21700 Å2
MethodPISA
2
C: Aac(3)-IIIb protein

D: Aac(3)-IIIb protein


Theoretical massNumber of molelcules
Total (without water)58,0382
Polymers58,0382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x+1/2,-y-1/2,-z1
Buried area2580 Å2
ΔGint-9 kcal/mol
Surface area21630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.478, 99.649, 207.605
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
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...
31(chain C and (resid 7 through 52 or resid 54...
41(chain D 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
12ASPASPASPASP(chain A and (resid 7 through 52 or resid 54...AA54 - 6754 - 67
13GLUGLUVALVAL(chain A and (resid 7 through 52 or resid 54...AA69 - 25269 - 252
14ALAALATHRTHR(chain A and (resid 7 through 52 or resid 54...AA254 - 271254 - 271
21SERSERLEULEU(chain B and (resid 7 through 52 or resid 54...BB7 - 527 - 52
22ASPASPASPASP(chain B and (resid 7 through 52 or resid 54...BB54 - 6754 - 67
23GLUGLUVALVAL(chain B and (resid 7 through 52 or resid 54...BB69 - 25269 - 252
24ALAALATHRTHR(chain B and (resid 7 through 52 or resid 54...BB254 - 271254 - 271
31SERSERLEULEU(chain C and (resid 7 through 52 or resid 54...CC7 - 527 - 52
32ASPASPASPASP(chain C and (resid 7 through 52 or resid 54...CC54 - 6754 - 67
33GLUGLUVALVAL(chain C and (resid 7 through 52 or resid 54...CC69 - 25269 - 252
34ALAALATHRTHR(chain C and (resid 7 through 52 or resid 54...CC254 - 271254 - 271
41SERSERLEULEU(chain D and (resid 7 through 52 or resid 54...DD7 - 527 - 52
42ASPASPASPASP(chain D and (resid 7 through 52 or resid 54...DD54 - 6754 - 67
43GLUGLUVALVAL(chain D and (resid 7 through 52 or resid 54...DD69 - 25269 - 252
44ALAALATHRTHR(chain D and (resid 7 through 52 or resid 54...DD254 - 271254 - 271

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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-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


Mass: 447.526 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H37N5O7 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 629 / 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: 3.1 Å3/Da / Density % sol: 60.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20-23% PEG 8000,0.1M di-ammonium phosphate and 0.1M MES, pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 58699 / % possible obs: 90.7 % / Redundancy: 4.4 % / Biso Wilson estimate: 23.52 Å2 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.035 / Rrim(I) all: 0.085 / Χ2: 0.379 / Net I/σ(I): 5.5 / Num. measured all: 258055
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.383.70.17355730.9780.0870.1940.23787.3
2.38-2.4840.18258060.9790.0880.2020.26290.7
2.48-2.594.10.17257590.9750.0830.1920.25290.5
2.59-2.734.10.15357580.9830.0740.170.26990.5
2.73-2.94.10.13557910.9870.0630.1490.26489.7
2.9-3.124.20.10756120.9890.0510.1180.30187.1
3.12-3.444.70.08660430.9960.0390.0950.37393.7
3.44-3.935.20.06561710.9970.0280.0710.36995.1
3.93-4.954.80.04960300.9980.0220.0530.49692
4.95-504.80.05361560.9960.0240.0590.79489.9

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Processing

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

6bc3


Resolution: 2.302→49.958 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.24
RfactorNum. reflection% reflection
Rfree0.229 1999 3.41 %
Rwork0.1949 --
obs0.1961 58615 90.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 92.65 Å2 / Biso mean: 25.1282 Å2 / Biso min: 5.58 Å2
Refinement stepCycle: final / Resolution: 2.302→49.958 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7960 0 62 629 8651
Biso mean--29.25 26.91 -
Num. residues----1060
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3160X-RAY DIFFRACTION4.698TORSIONAL
12B3160X-RAY DIFFRACTION4.698TORSIONAL
13C3160X-RAY DIFFRACTION4.698TORSIONAL
14D3160X-RAY DIFFRACTION4.698TORSIONAL
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 (%)
2.3024-2.360.27631330.22633747388085
2.36-2.42380.27261400.22353999413990
2.4238-2.49510.25031410.22023967410890
2.4951-2.57570.28281420.21673998414090
2.5757-2.66770.26511410.21174013415491
2.6677-2.77450.25441410.22054000414190
2.7745-2.90080.2621400.22943942408290
2.9008-3.05370.28951350.22873847398287
3.0537-3.2450.21531430.21494058420191
3.245-3.49550.25381480.2094193434194
3.4955-3.84710.22421520.17994292444496
3.8471-4.40350.19021480.1614192434093
4.4035-5.54690.16481460.15034111425790
5.5469-49.96970.20531490.1764257440690

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