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- PDB-4dt8: Crystal Structure of Aminoglycoside-2''-Phosphotransferase Type I... -

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Basic information

Entry
Database: PDB / ID: 4dt8
TitleCrystal Structure of Aminoglycoside-2''-Phosphotransferase Type IVa in Complex with Adenosine
ComponentsAPH(2'')-Id
KeywordsTRANSFERASE / Aminoglycoside kinase
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
ADENOSINE / APH(2'')-Id
Similarity search - Component
Biological speciesEnterococcus casseliflavus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsShi, K. / Berghuis, A.M.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural Basis for Dual Nucleotide Selectivity of Aminoglycoside 2''-Phosphotransferase IVa Provides Insight on Determinants of Nucleotide Specificity of Aminoglycoside Kinases.
Authors: Shi, K. / Berghuis, A.M.
History
DepositionFeb 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1May 9, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: APH(2'')-Id
B: APH(2'')-Id
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5986
Polymers72,9932
Non-polymers6054
Water3,549197
1
A: APH(2'')-Id
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7993
Polymers36,4971
Non-polymers3032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: APH(2'')-Id
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7993
Polymers36,4971
Non-polymers3032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-20 kcal/mol
Surface area28370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.664, 101.403, 73.588
Angle α, β, γ (deg.)90.00, 100.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 36496.551 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus casseliflavus (bacteria) / Gene: aph(2'')-Id / Production host: Escherichia coli (E. coli) / References: UniProt: O68183
#2: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.14 Å3/Da / Density % sol: 42.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100mM HEPES, 150mM potassium nitrate, 17% PEG 3350, 6% 2-propanol, 10% glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 27, 2011
RadiationMonochromator: Confocal dual reflection mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 31702 / Num. obs: 31670 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 7.3 % / Rsym value: 0.075 / Net I/σ(I): 27.1
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 5.5 / Rsym value: 0.3 / % possible all: 98.3

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→41.94 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.92 / SU B: 11.92 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.279 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24494 1686 5.1 %RANDOM
Rwork0.19003 ---
all0.19284 31670 --
obs0.19284 31670 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.924 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å2-0.05 Å2
2---0.24 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.15→41.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4811 0 40 197 5048
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.025009
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8551.9696792
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3875609
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.89625.041244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.85615866
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3151516
X-RAY DIFFRACTIONr_chiral_restr0.1220.2735
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213826
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.208 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 122 -
Rwork0.233 2252 -
obs--98.34 %
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)
13.50431.1111.15150.6319-0.57164.154-0.03630.1328-0.1419-0.0541-0.062-0.17080.04340.3440.09830.1248-0.02160.03770.15290.03040.200816.3936-5.536620.7039
21.6183-0.0154-0.30621.01220.17740.32460.0197-0.0597-0.0828-0.01690.04210.00910.0359-0.0576-0.06180.079-0.0319-0.02980.11240.02060.07344.781-10.149724.9932
31.32480.19380.41182.32761.36193.42640.00650.02320.02450.0933-0.07660.1898-0.11610.07480.07010.028-0.00680.00440.04950.01570.0682-9.9841-9.100537.641
43.8339-1.91391.0592.3425-0.52310.86320.00470.0628-0.0997-0.0368-0.01430.1056-0.08710.09330.00960.05280.0208-0.020.0478-0.00760.0912-4.323-39.227438.1879
51.60170.3525-0.10444.48410.57541.4736-0.0188-0.0735-0.02060.10210.0489-0.0613-0.03030.2434-0.030.01410.0073-0.01180.0930.01740.0513-6.2936-10.614735.911
62.581.12640.9294.5696-0.90751.97940.2094-0.3827-0.19340.6265-0.33480.16140.1073-0.10810.12540.1465-0.02840.04230.13170.00570.1139-12.0144-15.095344.9441
76.2343-4.1761-1.20165.55960.17860.3782-0.2531-0.2747-0.05670.23760.2076-0.11410.01730.03160.04540.1846-0.0079-0.00820.1287-0.03040.0323-0.9057-29.746843.0279
810.4833-2.25330.65241.0196-0.66886.3289-0.1163-0.61090.47060.29150.0745-0.85960.71520.92260.04180.43390.176-0.43110.3508-0.07841.242218.6982-44.232223.8974
91.04120.40710.50592.73860.95641.9057-0.02970.0028-0.0565-0.08320.0026-0.39180.22040.07180.02710.09640.00480.04970.04850.00510.07868.7439-40.943215.6026
101.3079-0.3137-0.07021.96081.41842.78640.06360.0724-0.09930.0227-0.06490.0557-0.0553-0.02190.00130.1092-0.03690.03380.0358-0.00410.0389-0.9425-43.7163-1.4482
113.02160.4811-0.36612.6489-0.17140.7989-0.03340.0490.04470.06840.05060.38710.23990.2371-0.01720.21210.06570.02180.0830.01040.09560.8529-12.7008-0.3548
121.8076-0.9750.80734.51390.36991.6991-0.00610.0265-0.00830.17470.0168-0.1249-0.1060.0583-0.01070.1233-0.02960.02680.05630.00180.03721.6371-41.15991.7696
131.81720.5993-0.80343.2623-0.17991.29950.02270.25270.0658-0.0634-0.04330.0446-0.2213-0.07160.02060.1948-0.0231-0.02310.0893-0.00390.0361-0.8898-37.3126-8.7219
145.09184.04022.4395.91912.30221.7644-0.18920.17970.0461-0.17460.3089-0.30860.06670.1319-0.11970.26140.07750.05940.1288-0.02010.12846.8205-22.4498-2.9833
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 23
2X-RAY DIFFRACTION2A24 - 97
3X-RAY DIFFRACTION3A98 - 144
4X-RAY DIFFRACTION4A145 - 189
5X-RAY DIFFRACTION5A190 - 225
6X-RAY DIFFRACTION6A226 - 253
7X-RAY DIFFRACTION7A254 - 301
8X-RAY DIFFRACTION8B1 - 23
9X-RAY DIFFRACTION9B24 - 97
10X-RAY DIFFRACTION10B98 - 144
11X-RAY DIFFRACTION11B145 - 189
12X-RAY DIFFRACTION12B190 - 225
13X-RAY DIFFRACTION13B226 - 253
14X-RAY DIFFRACTION14B254 - 296

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