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- PDB-7bxz: Crystal structure of the aminoglycoside 6'-N-acetyltransferase fr... -

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Basic information

Entry
Database: PDB / ID: 7bxz
TitleCrystal structure of the aminoglycoside 6'-N-acetyltransferase from Enterococcus faecium
ComponentsAminoglycoside 6'-N-acetyltransferase
KeywordsTRANSFERASE / aminoglycoside acetyltransferase / Enterococcus faecium / acetyl-CoA
Function / homologyacyltransferase activity, transferring groups other than amino-acyl groups / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aac(6')-Ii protein
Function and homology information
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.502 Å
AuthorsKwon, S. / Park, H.H.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2017M3A9D8062960 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2018R1A4A1023822 Korea, Republic Of
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Structural analysis of a novel substrate-free form of the aminoglycoside 6'-N-acetyltransferase from Enterococcus faecium.
Authors: Jang, H. / Kwon, S. / Jeong, C.S. / Lee, C.W. / Hwang, J. / Jung, K.H. / Lee, J.H. / Park, H.H.
History
DepositionApr 21, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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: Aminoglycoside 6'-N-acetyltransferase
B: Aminoglycoside 6'-N-acetyltransferase
C: Aminoglycoside 6'-N-acetyltransferase


Theoretical massNumber of molelcules
Total (without water)62,1013
Polymers62,1013
Non-polymers00
Water1,45981
1
A: Aminoglycoside 6'-N-acetyltransferase
B: Aminoglycoside 6'-N-acetyltransferase


Theoretical massNumber of molelcules
Total (without water)41,4002
Polymers41,4002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-19 kcal/mol
Surface area17220 Å2
MethodPISA
2
C: Aminoglycoside 6'-N-acetyltransferase

C: Aminoglycoside 6'-N-acetyltransferase


Theoretical massNumber of molelcules
Total (without water)41,4002
Polymers41,4002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
Buried area2710 Å2
ΔGint-22 kcal/mol
Surface area17160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.426, 90.317, 102.151
Angle α, β, γ (deg.)90.000, 96.080, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 7 or (resid 8...
21(chain B and (resid 1 through 21 or (resid 22...
31(chain C and (resid 1 through 7 or (resid 8...

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
11METMETASPASP(chain A and (resid 1 through 7 or (resid 8...AA1 - 71 - 7
12ARGARGARGARG(chain A and (resid 1 through 7 or (resid 8...AA88
13METMETASPASP(chain A and (resid 1 through 7 or (resid 8...AA1 - 1801 - 180
14METMETASPASP(chain A and (resid 1 through 7 or (resid 8...AA1 - 1801 - 180
15METMETASPASP(chain A and (resid 1 through 7 or (resid 8...AA1 - 1801 - 180
16METMETASPASP(chain A and (resid 1 through 7 or (resid 8...AA1 - 1801 - 180
21METMETLEULEU(chain B and (resid 1 through 21 or (resid 22...BB1 - 211 - 21
22ARGARGLEULEU(chain B and (resid 1 through 21 or (resid 22...BB22 - 2322 - 23
23METMETASPASP(chain B and (resid 1 through 21 or (resid 22...BB1 - 1801 - 180
24METMETASPASP(chain B and (resid 1 through 21 or (resid 22...BB1 - 1801 - 180
25METMETASPASP(chain B and (resid 1 through 21 or (resid 22...BB1 - 1801 - 180
26METMETASPASP(chain B and (resid 1 through 21 or (resid 22...BB1 - 1801 - 180
31METMETASPASP(chain C and (resid 1 through 7 or (resid 8...CC1 - 71 - 7
32ARGARGARGARG(chain C and (resid 1 through 7 or (resid 8...CC88
33METMETASPASP(chain C and (resid 1 through 7 or (resid 8...CC1 - 1801 - 180
34METMETASPASP(chain C and (resid 1 through 7 or (resid 8...CC1 - 1801 - 180
35METMETASPASP(chain C and (resid 1 through 7 or (resid 8...CC1 - 1801 - 180

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Components

#1: Protein Aminoglycoside 6'-N-acetyltransferase / Aac(6')-Ii protein


Mass: 20700.213 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecium (bacteria) / Gene: aac(6')-Ii / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q47764
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.53 Å3/Da / Density % sol: 51.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 50 mM HEPES-Na (pH 7.0), 10 mM magnesium chloride, 1.6 M ammonium sulfate

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.977872 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977872 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 21196 / % possible obs: 98.9 % / Redundancy: 7 % / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.026 / Rrim(I) all: 0.069 / Χ2: 0.403 / Net I/σ(I): 5.3 / Num. measured all: 148028
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.546.70.47210410.8920.1960.5120.33797.7
2.54-2.596.40.42110510.9210.1810.4590.33899
2.59-2.646.20.36110550.9470.1590.3950.33497.8
2.64-2.696.70.33410580.9490.140.3630.35499.2
2.69-2.756.50.2910330.9480.1230.3150.36598.6
2.75-2.8270.25310570.9690.1030.2730.36598.9
2.82-2.897.50.22410420.9810.0870.2410.38598.5
2.89-2.967.50.19210670.9840.0750.2060.3898.7
2.96-3.057.40.15510390.9870.0610.1670.39799.2
3.05-3.157.40.12110910.9920.0470.130.41798.6
3.15-3.267.30.10410230.9950.0410.1120.41798.6
3.26-3.397.30.08710590.9960.0340.0940.43599.3
3.39-3.557.30.07210740.9970.0280.0770.43999.3
3.55-3.737.20.06210560.9970.0240.0670.45299.5
3.73-3.977.20.05110570.9980.020.0550.43699.1
3.97-4.276.90.04710860.9980.0190.050.45999.2
4.27-4.76.50.0410590.9990.0170.0430.4599.6
4.7-5.3860.03710620.9980.0170.0410.43699
5.38-6.767.30.03910790.9990.0150.0420.42999.4
6.76-307.40.0311070.9990.0120.0320.4199.6

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
SCALEPACKdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6G9P

6g9p


Resolution: 2.502→29.895 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 28.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2653 1037 4.9 %
Rwork0.2259 20143 -
obs0.2278 21180 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.63 Å2 / Biso mean: 57.7978 Å2 / Biso min: 22.39 Å2
Refinement stepCycle: final / Resolution: 2.502→29.895 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4166 0 0 81 4247
Biso mean---50.87 -
Num. residues----532
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1536X-RAY DIFFRACTION10.779TORSIONAL
12B1536X-RAY DIFFRACTION10.779TORSIONAL
13C1536X-RAY DIFFRACTION10.779TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.502-2.63350.31291400.2614284898
2.6335-2.79840.32861500.2778284899
2.7984-3.01430.32651540.2741285599
3.0143-3.31730.28331460.2521287899
3.3173-3.79650.29821500.2248290099
3.7965-4.780.23161500.1946287899
4.78-29.8950.22441470.2121293699
Refinement TLS params.Method: refined / Origin x: 38.0588 Å / Origin y: 21.8801 Å / Origin z: 27.1899 Å
111213212223313233
T0.2395 Å2-0.0726 Å20.0298 Å2-0.2002 Å20.0161 Å2--0.2161 Å2
L0.4577 °20.3382 °20.4351 °2-0.3553 °20.2931 °2--0.8998 °2
S0.1408 Å °0.0044 Å °0.0092 Å °0.1706 Å °-0.0985 Å °0.0473 Å °-0.021 Å °-0.0047 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 180
2X-RAY DIFFRACTION1allB1 - 180
3X-RAY DIFFRACTION1allC1 - 180
4X-RAY DIFFRACTION1allS1 - 89

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