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- PDB-3tm0: Crystal Structure of 3',5"-Aminoglycoside Phosphotransferase Type... -

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Basic information

Entry
Database: PDB / ID: 3tm0
TitleCrystal Structure of 3',5"-Aminoglycoside Phosphotransferase Type IIIa AMPPNP Butirosin A Complex
ComponentsAminoglycoside 3'-phosphotransferase
KeywordsTRANSFERASE/ANTIBIOTIC / protein kinase / phosphorylation / TRANSFERASE-ANTIBIOTIC complex
Function / homology
Function and homology information


kanamycin kinase / kanamycin kinase activity / phosphorylation / response to antibiotic / ATP binding
Similarity search - Function
Aminoglycoside 3-phosphotransferase / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Chem-B31 / Aminoglycoside 3'-phosphotransferase
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBerghuis, A.M. / Fong, D.H.
Citation
Journal: Antimicrob.Agents Chemother. / Year: 2009
Title: Structural basis of APH(3')-IIIa-mediated resistance to N1-substituted aminoglycoside antibiotics.
Authors: Fong, D.H. / Berghuis, A.M.
#1: Journal: To be Published
Title: Crystal structure of 3'-aminoglycoside phosphotransferase type IIIa in complex with AMPPNP and an aminoglycoside product, 5"-monophosphorylated butirosin
Authors: Berghuis, A.M. / Fong, D.H.
History
DepositionAug 30, 2011Deposition site: RCSB / Processing site: RCSB
SupersessionOct 19, 2011ID: 3H8P
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminoglycoside 3'-phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9915
Polymers30,8811
Non-polymers1,1104
Water3,171176
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.112, 80.112, 110.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Aminoglycoside 3'-phosphotransferase / 3' / 5"-aminoglycoside phosphotransferase type IIIa / APH(3')III / Kanamycin kinase / type III / ...3' / 5"-aminoglycoside phosphotransferase type IIIa / APH(3')III / Kanamycin kinase / type III / Neomycin-kanamycin phosphotransferase type III


Mass: 30880.850 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: aph(3')-iiia, aphA / Plasmid: pET-22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A3Y5, kanamycin kinase
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-B31 / (2S)-4-amino-N-[(1R,2S,3R,4R,5S)-5-amino-4-[(2,6-diamino-2,6-dideoxy-alpha-D-glucopyranosyl)oxy]-2-hydroxy-3-(beta-D-xylofuranosyloxy)cyclohexyl]-2-hydroxybutanamide / Butirosin A / Butirosin


Mass: 555.577 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H41N5O12 / Comment: antibiotic*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.86 Å3/Da / Density % sol: 57.01 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 40% PEG600, 0.1 M sodium acetate, 0.2 M magnesium chloride, 3% D(+)-sucrose, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.072 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Mar 4, 2001 / Details: mirrors
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 19062 / % possible obs: 87.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.1 % / Biso Wilson estimate: 31.32 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 42.03
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 10.3 / Num. unique all: 1066 / % possible all: 50.3

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Processing

Software
NameVersionClassification
CBASSdata collection
AMoREphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1L8T

1l8t


Resolution: 2.1→39.571 Å / SU ML: 0.64 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1923 10.1 %RANDOM
Rwork0.1792 ---
obs0.1837 19035 87.78 %-
all-21685 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.882 Å2 / ksol: 0.36 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.0686 Å2-0 Å20 Å2
2---0.0686 Å20 Å2
3---0.1372 Å2
Refinement stepCycle: LAST / Resolution: 2.1→39.571 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2170 0 71 176 2417
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012300
X-RAY DIFFRACTIONf_angle_d1.1053115
X-RAY DIFFRACTIONf_dihedral_angle_d13.967858
X-RAY DIFFRACTIONf_chiral_restr0.07335
X-RAY DIFFRACTIONf_plane_restr0.004390
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.15240.2434750.1967664X-RAY DIFFRACTION49
2.1524-2.21060.2339840.1867768X-RAY DIFFRACTION56
2.2106-2.27560.2333870.1836858X-RAY DIFFRACTION63
2.2756-2.3490.25771100.1946986X-RAY DIFFRACTION72
2.349-2.4330.28241330.18631216X-RAY DIFFRACTION89
2.433-2.53040.26181370.20031374X-RAY DIFFRACTION99
2.5304-2.64550.24681620.20641351X-RAY DIFFRACTION100
2.6455-2.7850.28071570.19871379X-RAY DIFFRACTION100
2.785-2.95940.24481600.19061362X-RAY DIFFRACTION100
2.9594-3.18780.2391520.19231402X-RAY DIFFRACTION100
3.1878-3.50840.22511620.18411395X-RAY DIFFRACTION100
3.5084-4.01570.19731690.16021402X-RAY DIFFRACTION100
4.0157-5.05770.19941510.1421436X-RAY DIFFRACTION100
5.0577-39.57790.20041840.19251519X-RAY DIFFRACTION100
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)
11.3307-0.34691.03710.0904-0.27010.80650.024-0.7050.62370.7274-0.0135-0.1994-0.3104-0.77540.01760.3556-0.0102-0.03090.2984-0.07140.291240.767958.490728.5536
21.26580.18840.14690.10090.17280.3411-0.0151-0.15990.4117-0.78210.08310.0928-0.9974-0.78610.14530.52040.1956-0.05470.32870.02850.236741.436262.708317.3249
32.1604-0.201-3.10620.3441-0.14675.0491-0.00290.5614-0.79870.1476-0.5099-0.55621.18120.7673-0.27990.44880.0332-0.2520.5278-0.08540.636142.157345.737712.4015
40.33760.16760.05050.08530.02250.0090.08850.02820.0401-0.09750.21270.78140.6456-0.26520.05280.34930.0034-0.01040.1672-0.02450.208544.728344.551719.3471
50.68410.09480.01130.87880.65960.5017-0.0093-0.09680.07950.16370.00410.163-0.1701-0.1170.00070.1720.0036-0.00430.17590.00260.172147.675151.504519.6999
60.42970.201-0.00621.5689-0.24570.0156-0.09150.0287-0.08340.12020.023-0.0939-0.0373-0.0688-0.00020.18550.0119-0.02880.1259-0.01780.168655.711952.580721.9993
70.1460.0360.08670.03850.0860.1977-0.10040.483-0.2247-0.9572-0.1286-0.07840.29780.3944-0.00030.49670.0127-0.04920.26840.04070.234554.089743.63690.513
81.49720.62150.17444.0506-0.01130.79650.85460.1491-0.4876-0.13050.52931.3621.0746-0.73460.16021.1517-0.0255-0.31850.49430.10360.487557.973135.305-4.8528
90.3988-0.16380.16950.8118-0.15660.16040.1290.12680.1895-0.3055-0.2998-0.70280.28480.2502-0.0030.28780.01590.0510.24070.06050.251168.704242.448812.8962
100.2202-0.1513-0.15220.18190.09130.19240.0094-0.1428-0.05070.16530.1363-0.06490.02180.04380.00470.17030.0045-0.02660.1870.08190.225255.354833.400730.2522
110.15880.02410.10270.16470.29590.54570.15840.3429-0.15240.6867-0.38560.26740.0351-0.14540.01370.52950.0168-0.03690.6371-0.07250.503546.701720.935819.908
120.632-0.4644-0.48360.39370.48310.72640.0254-0.09150.5092-0.02460.39950.01230.3892-0.05240.21920.18840.0322-0.14890.14220.20850.351261.351324.228527.4105
130.29290.10940.11310.3876-0.23070.24360.09390.2618-0.1394-0.3816-0.1275-0.1740.05660.03590.00010.34740.0258-0.00250.17720.00250.172760.880742.851811.1738
140.3140.06030.17330.1874-0.14820.26510.05890.159-0.0704-0.3073-0.0709-0.16710.1599-0.0886-0.00010.25960.01520.00080.12640.01530.163563.163238.677314.5244
150.09830.07080.00890.05780.02110.01780.00450.4611-0.3379-0.6751-0.20780.28950.1244-0.51580.00080.7170.0947-0.01410.3662-0.05630.304959.626427.27512.0574
160.70030.40380.17760.21770.07820.38830.16920.2199-0.2375-0.2966-0.0043-0.10390.0188-0.10390.00020.31930.07630.05320.13090.01370.26968.119127.064411.0264
170.13510.0719-0.010.04960.02760.08130.3049-0.0058-0.3712-0.2859-0.07680.23550.04150.52590.00240.2717-0.0343-0.07090.1580.01460.250654.337430.204421.5167
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 2:10)
2X-RAY DIFFRACTION2(chain 'A' and resid 11:19)
3X-RAY DIFFRACTION3(chain 'A' and resid 20:25)
4X-RAY DIFFRACTION4(chain 'A' and resid 26:32)
5X-RAY DIFFRACTION5(chain 'A' and resid 33:54)
6X-RAY DIFFRACTION6(chain 'A' and resid 55:94)
7X-RAY DIFFRACTION7(chain 'A' and resid 95:103)
8X-RAY DIFFRACTION8(chain 'A' and resid 104:110)
9X-RAY DIFFRACTION9(chain 'A' and resid 111:132)
10X-RAY DIFFRACTION10(chain 'A' and resid 133:153)
11X-RAY DIFFRACTION11(chain 'A' and resid 154:166)
12X-RAY DIFFRACTION12(chain 'A' and resid 167:183)
13X-RAY DIFFRACTION13(chain 'A' and resid 184:200)
14X-RAY DIFFRACTION14(chain 'A' and resid 201:226)
15X-RAY DIFFRACTION15(chain 'A' and resid 227:238)
16X-RAY DIFFRACTION16(chain 'A' and resid 239:259)
17X-RAY DIFFRACTION17(chain 'A' and resid 260:264)

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