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- PDB-6iy9: Crystal structure of aminoglycoside 7"-phoshotransferase-Ia (APH(... -

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Basic information

Entry
Database: PDB / ID: 6iy9
TitleCrystal structure of aminoglycoside 7"-phoshotransferase-Ia (APH(7")-Ia/HYG) from Streptomyces hygroscopicus complexed with hygromycin B
ComponentsHygromycin-B 7''-O-kinase
KeywordsTRANSFERASE / Kinase / Complex
Function / homology
Function and homology information


hygromycin-B 7''-O-kinase / hygromycin-B 7''-O-phosphotransferase activity / response to antibiotic / ATP binding
Similarity search - Function
Hygromycin-B kinase / Aminoglycoside phosphotransferase / Phosphotransferase enzyme family / Protein kinase-like domain superfamily
Similarity search - Domain/homology
CITRATE ANION / HYGROMYCIN B VARIANT / Hygromycin-B 7''-O-kinase
Similarity search - Component
Biological speciesStreptomyces hygroscopicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsTakenoya, M. / Shimamura, T. / Yamanaka, R. / Adachi, Y. / Ito, S. / Sasaki, Y. / Nakamura, A. / Yajima, S.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2019
Title: Structural basis for the substrate recognition of aminoglycoside 7''-phosphotransferase-Ia from Streptomyces hygroscopicus.
Authors: Takenoya, M. / Shimamura, T. / Yamanaka, R. / Adachi, Y. / Ito, S. / Sasaki, Y. / Nakamura, A. / Yajima, S.
History
DepositionDec 14, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hygromycin-B 7''-O-kinase
B: Hygromycin-B 7''-O-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,4328
Polymers76,5852
Non-polymers1,8486
Water37821
1
A: Hygromycin-B 7''-O-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2164
Polymers38,2921
Non-polymers9243
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint2 kcal/mol
Surface area14780 Å2
MethodPISA
2
B: Hygromycin-B 7''-O-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2164
Polymers38,2921
Non-polymers9243
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint2 kcal/mol
Surface area14940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.590, 151.590, 151.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number195
Space group name H-MP23

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Components

#1: Protein Hygromycin-B 7''-O-kinase / Aminoglycoside phosphotransferase 7"-Ia / APH(7'') / Hygromycin B phosphotransferase / Hygromycin-B kinase


Mass: 38292.324 Da / Num. of mol.: 2 / Mutation: D63G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces hygroscopicus (bacteria) / Gene: hyg / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: P09979, hygromycin-B 7''-O-kinase
#2: Chemical ChemComp-HY0 / HYGROMYCIN B VARIANT / (2R,3'R,3aS,4S,4'S,5'R,6R,6'R,7S,7aS)-4-[(1R,2S,3R,5S,6R)-3-azanyl-2,6-dihydroxy-5-(methylamino)cyclohexyl]oxy-6'-[(1S)-1-azanyl-2-hydroxy-ethyl]-6-(hydroxymethyl)spiro[4,6,7,7a-tetrahydro-3aH-[1,3]dioxolo[4,5-c]pyran-2,2'-oxane]-3',4',5',7-tetrol


Mass: 527.520 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H37N3O13
#3: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES / CHES (buffer)


Mass: 207.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#4: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 3.8 Å3/Da / Density % sol: 67.66 %
Description: The entry contains friedel pairs in F_plus/minus columns
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 0.1 M CHES, pH 8.8, 1.38-1.40 M sodium citrate tribasic

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 45592 / % possible obs: 100 % / Redundancy: 62.7 % / CC1/2: 1 / Rmerge(I) obs: 0.132 / Net I/σ(I): 31.2
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 64.6 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 6572 / CC1/2: 0.5 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.15.2refinement
XDSdata reduction
XSCALEdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→47.9 Å / Cross valid method: THROUGHOUT
Details: The entry contains friedel pairs in F_plus/minus columns
RfactorNum. reflection% reflectionSelection details
Rfree0.251 2330 5.1 %Random selection
Rwork0.225 ---
obs0.226 45592 100 %-
Displacement parametersBiso mean: 103.26 Å2
Refinement stepCycle: LAST / Resolution: 2.4→47.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5137 0 124 21 5282
LS refinement shellResolution: 2.4→2.45 Å
RfactorNum. reflection% reflection
Rfree0.372 --
Rwork0.329 --
obs-2676 100 %
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)
15.06761.1551-3.2666.89766.30927.7483-0.82080.7735-1.0639-0.54430.6878-0.25540.86630.76750.0991.2455-0.02890.14530.6335-0.06490.75838.8397-13.261830.366
22.73980.05360.6133.6844-1.40425.95540.06410.4326-0.2557-0.4831-0.3861-0.67630.58741.92550.16480.67090.20590.25441.11810.08020.545825.5847-4.483846.2312
39.51963.05270.39796.0958-0.70173.35760.40330.15581.55840.72260.0020.2562-1.8323-0.7656-0.3522.16640.31670.04721.04620.08610.6663-5.674337.533264.4016
43.8618-0.8989-2.30393.8828-0.7541.94350.02180.40630.39310.0091-0.06440.0299-1.4489-0.0239-0.01421.5604-0.0434-0.13440.65470.03950.4682.300927.126959.7107
53.44430.2778-0.33332.78770.66735.3899-0.1784-0.45250.29230.18080.0397-0.4966-1.29671.54220.13191.0727-0.4145-0.10.99070.09260.472121.902421.155167.2464
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 4 through 88 )
2X-RAY DIFFRACTION2chain 'B' and (resid 89 through 327 )
3X-RAY DIFFRACTION3chain 'A' and (resid 3 through 59 )
4X-RAY DIFFRACTION4chain 'A' and (resid 60 through 136 )
5X-RAY DIFFRACTION5chain 'A' and (resid 137 through 327 )

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