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- PDB-5c4k: APH(2")-IVa in complex with GET (G418) at room temperature -

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Basic information

Entry
Database: PDB / ID: 5c4k
TitleAPH(2")-IVa in complex with GET (G418) at room temperature
ComponentsAPH(2'')-Id
KeywordsTRANSFERASE / Aminoglycoside phosphotransferase / antibiotic resistance
Function / homology
Function and homology information


nucleotide binding / metal ion binding
Similarity search - Function
Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 / Aminoglycoside phosphotransferase (APH), C-terminal lobe / Aminoglycoside phosphotransferase / Phosphotransferase enzyme family / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase-like domain superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
GENETICIN / APH(2'')-Id
Similarity search - Component
Biological speciesEnterococcus casseliflavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsKaplan, E. / Guichou, J.F. / Berrou, K. / Chaloin, L. / Leban, N. / Lallemand, P. / Barman, T. / Serpersu, E.H. / Lionne, C.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyFDT20140931113 France
CitationJournal: Biochim.Biophys.Acta / Year: 2016
Title: Aminoglycoside binding and catalysis specificity of aminoglycoside 2-phosphotransferase IVa: A thermodynamic, structural and kinetic study.
Authors: Kaplan, E. / Guichou, J.F. / Chaloin, L. / Kunzelmann, S. / Leban, N. / Serpersu, E.H. / Lionne, C.
History
DepositionJun 18, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / 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 / _pdbx_audit_support.funding_organization / _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: APH(2'')-Id
B: APH(2'')-Id
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,6883
Polymers75,1922
Non-polymers4971
Water00
1
A: APH(2'')-Id
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0922
Polymers37,5961
Non-polymers4971
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: APH(2'')-Id


Theoretical massNumber of molelcules
Total (without water)37,5961
Polymers37,5961
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.703, 64.941, 78.870
Angle α, β, γ (deg.)90.000, 90.730, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 2 - 296 / Label seq-ID: 22 - 316

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein APH(2'')-Id


Mass: 37595.852 Da / Num. of mol.: 2 / Mutation: E26Q, E30K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus casseliflavus (bacteria) / Gene: aph(2'')-Id / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O68183
#2: Chemical ChemComp-GET / GENETICIN / G418


Mass: 496.552 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H40N4O10 / Comment: antibiotic*YM

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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: 2.89 Å3/Da / Density % sol: 57.37 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 12% PEG3350, 50-90 mM Ammonium citrate / PH range: 7.0-7.9

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Data collection

DiffractionMean temperature: 291.15 K / Ambient temp details: in situ
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9797 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.9→42.44 Å / Num. all: 17997 / Num. obs: 16269 / % possible obs: 90.4 % / Redundancy: 1.6 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 2.6
Reflection shellResolution: 2.9→3.05 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 1.4 / % possible all: 93.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
SCALAdata scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4n57

4n57


Resolution: 3.05→78.86 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.955 / SU B: 40.11 / SU ML: 0.307 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.394 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1992 721 5.2 %RANDOM
Rwork0.1591 ---
obs0.1612 13126 89.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 174.94 Å2 / Biso mean: 90.908 Å2 / Biso min: 41.49 Å2
Baniso -1Baniso -2Baniso -3
1-2.3 Å2-0 Å2-0.93 Å2
2---3.13 Å2-0 Å2
3---0.85 Å2
Refinement stepCycle: final / Resolution: 3.05→78.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4914 0 34 0 4948
Biso mean--123.12 --
Num. residues----593
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195086
X-RAY DIFFRACTIONr_bond_other_d0.0040.024810
X-RAY DIFFRACTIONr_angle_refined_deg1.5151.976864
X-RAY DIFFRACTIONr_angle_other_deg0.978311135
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2365595
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.48425260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.38815940
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.621520
X-RAY DIFFRACTIONr_chiral_restr0.0880.2733
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215676
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021180
X-RAY DIFFRACTIONr_mcbond_it2.2073.5872380
X-RAY DIFFRACTIONr_mcbond_other2.2053.5852379
X-RAY DIFFRACTIONr_mcangle_it3.5265.3782975
Refine LS restraints NCS

Ens-ID: 1 / Number: 17878 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.05→3.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 61 -
Rwork0.305 991 -
all-1052 -
obs--94.69 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
19.0803-9.6679-7.20416.29931.267916.49380.01730.9963-0.6097-0.2877-0.11022.41990.563-2.34270.09290.3874-0.0250.10690.6950.04471.1459-16.51759.108749.1744
27.6388-1.5085-0.84778.8531-0.48644.5176-0.2193-0.87090.26261.6140.15180.94370.1108-0.8750.06740.5265-0.0320.23380.420.01010.3822-10.49326.387755.7303
311.391-3.44311.53168.799-2.06647.73080.16830.33840.04180.295-0.14040.74920.621-0.3588-0.02780.44-0.11240.10040.31590.12990.2939-6.0651-0.061948.106
425.1924-13.3993-9.732126.5378-8.756622.01140.170.015-1.17730.907-0.2775-0.33932.23340.33850.10741.25710.0628-0.250.31020.03480.55933.9804-9.33850.0838
56.5723-1.734-3.31634.7084-1.44045.9764-0.2581-0.2591-0.38911.17360.37290.12340.2032-0.0321-0.11480.60390.0036-0.06650.23740.00420.23740.0490.780149.4185
62.96370.68970.306711.2686-1.4045.90370.1715-0.1990.17880.5756-0.2184-1.23370.31280.78710.04690.30520.1282-0.06180.45810.03060.698813.8831-1.783340.1162
710.7432-3.75334.96588.6449-5.62039.37910.30430.3458-0.5177-1.01720.12961.37830.8535-1.0621-0.43390.60290.0019-0.26520.3287-0.02040.5132-10.296-3.878818.4609
85.7418-1.24471.33895.1421-1.11054.80110.15521.1117-0.0891-1.1329-0.27070.30650.15630.13830.11560.35540.01530.0320.29380.02410.32632.3573-5.865521.0613
93.92820.1667-0.39097.69060.80458.3445-0.04050.37060.7917-0.20930.084-0.8979-0.89240.6823-0.04350.22090.0016-0.0340.23690.09420.426912.72662.967334.671
108.8054-1.87073.04978.3440.83626.0823-0.1249-0.17250.96-0.9143-0.24490.6979-0.7674-0.65750.36990.64020.2058-0.01710.38750.09490.4896-6.40986.333622.9511
1118.54625.54082.830112.92596.92274.15630.3229-2.27830.0491.829-0.4893-0.32020.6796-0.45720.16640.53950.0134-0.2510.76140.15290.549552.019622.86391.5404
128.5958-0.31030.71027.62972.12527.38410.1337-0.23180.39680.2593-0.1894-1.5037-0.09780.65990.05560.2134-0.0419-0.04170.47570.31930.63355.434719.947282.9881
137.78042.52695.719714.01615.060521.20760.662-0.0499-0.97940.187-0.65-0.49550.6552-0.3238-0.01190.41420.002-0.01830.47320.33580.60945.02026.921579.6213
148.32090.34814.00316.902-0.62976.42060.4742-0.0936-0.85560.2843-0.2958-0.970.43950.0354-0.17840.34730.10050.05780.4250.27650.593549.65589.219577.9419
157.4303-0.67673.87635.31030.36365.7954-0.13121.15690.8111-1.3509-0.5014-0.1495-0.75760.12690.63260.70310.17070.05550.67760.31210.384440.015622.585865.095
167.7198-4.49330.664310.98730.35514.76070.14360.9377-0.7873-0.9417-0.39050.19240.42920.2740.24690.44060.1460.03920.5532-0.08870.390236.9744.060367.0961
175.6848-3.0492-3.30425.62414.43095.415-0.7173-0.827-0.90771.2798-0.31511.26640.5843-0.24421.03240.76220.08380.32150.5246-0.10610.685119.24538.436988.0395
187.12491.0268-1.24338.5401-0.70455.10060.19970.68180.8401-0.3998-0.30530.6994-0.7017-0.10250.10560.44950.1844-0.09780.44640.05170.296833.670117.334568.9198
196.19612.6223-3.88835.81430.74975.74690.34720.00620.63040.2054-0.44131.0281-0.2802-0.00170.09420.40.2389-0.07270.506-0.10840.672523.811914.936676.6167
2010.50024.7357-5.87269.5418-1.28138.18191.5206-1.27941.69871.4781-0.90541.314-1.1161.1578-0.61520.8501-0.24510.5090.5374-0.58090.898820.982925.105991.5183
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 6
2X-RAY DIFFRACTION2A7 - 38
3X-RAY DIFFRACTION3A39 - 63
4X-RAY DIFFRACTION4A64 - 68
5X-RAY DIFFRACTION5A69 - 107
6X-RAY DIFFRACTION6A108 - 144
7X-RAY DIFFRACTION7A145 - 168
8X-RAY DIFFRACTION8A169 - 199
9X-RAY DIFFRACTION9A200 - 264
10X-RAY DIFFRACTION10A265 - 297
11X-RAY DIFFRACTION11B2 - 6
12X-RAY DIFFRACTION12B7 - 50
13X-RAY DIFFRACTION13B51 - 68
14X-RAY DIFFRACTION14B69 - 89
15X-RAY DIFFRACTION15B90 - 122
16X-RAY DIFFRACTION16B123 - 139
17X-RAY DIFFRACTION17B140 - 190
18X-RAY DIFFRACTION18B191 - 247
19X-RAY DIFFRACTION19B248 - 284
20X-RAY DIFFRACTION20B285 - 298

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