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- PDB-4dt9: Crystal Structure of Aminoglycoside-2''-Phosphotransferase Type I... -

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Basic information

Entry
Database: PDB / ID: 4dt9
TitleCrystal Structure of Aminoglycoside-2''-Phosphotransferase Type IVa in Complex with Guanosine
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
GUANOSINE / APH(2'')-Id
Similarity search - Component
Biological speciesEnterococcus casseliflavus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 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)73,5604
Polymers72,9932
Non-polymers5662
Water3,603200
1
A: APH(2'')-Id
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7802
Polymers36,4971
Non-polymers2831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: APH(2'')-Id
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7802
Polymers36,4971
Non-polymers2831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-2 kcal/mol
Surface area28350 Å2
Unit cell
Length a, b, c (Å)42.252, 101.288, 73.389
Angle α, β, γ (deg.)90.00, 100.00, 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-GMP / GUANOSINE


Mass: 283.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.12 Å3/Da / Density % sol: 41.95 %
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: Oct 4, 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: 2.1→50 Å / Num. all: 33771 / Num. obs: 33433 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 3.3 % / Rsym value: 0.074 / Net I/σ(I): 15.9
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 4.1 / Rsym value: 0.32 / % possible all: 89

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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: 2.1→34.04 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.935 / SU B: 10.757 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.241 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24204 1764 5 %RANDOM
Rwork0.18152 ---
all0.18459 33433 --
obs0.18459 33433 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.738 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å2-0.18 Å2
2---0.14 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→34.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4784 0 40 200 5024
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.024987
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.871.9696766
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4455608
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.22425.164244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.97915861
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2181515
X-RAY DIFFRACTIONr_chiral_restr0.1290.2732
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213815
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: 2.1→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 95 -
Rwork0.217 2175 -
obs--88.98 %
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)
17.23343.8016-0.73149.8897-0.07944.4902-0.20370.80930.2876-0.84220.18811.91580.5352-0.96870.01560.3528-0.1309-0.22910.480.02520.6015-4.58228.68812.8637
22.0139-0.54780.66771.7766-0.74761.24310.0297-0.0319-0.0915-0.05070.02890.23630.1415-0.0223-0.05860.1265-0.00040.03520.08090.01040.08456.061111.757520.6696
30.7731-0.0254-0.35142.228-0.91762.69510.0745-0.0924-0.0970.0052-0.0302-0.0997-0.15980.0539-0.04430.07590.01940.0480.10440.01420.096515.58168.875537.6293
42.3507-1.39420.10723.02190.3171.5022-0.0385-0.1316-0.02850.04340.0745-0.16530.1495-0.1974-0.0360.1612-0.05340.01720.05370.0010.097714.074139.815436.5832
50.87340.29080.97443.4263-0.63251.3739-0.0678-0.0143-0.0336-0.04550.13930.0838-0.0737-0.0937-0.07150.13610.02340.04040.11640.02030.068512.941411.372134.4665
61.16570.29550.65144.1538-0.60210.581-0.0147-0.34060.08010.1806-0.02710.128-0.155-0.15030.04170.2448-0.00890.01380.19070.00470.088715.806815.165245.152
77.4521-5.36743.11826.1619-2.62151.4445-0.0537-0.1923-0.11050.19450.18940.34120.0788-0.1116-0.13570.2921-0.04360.04680.09390.01520.11138.075830.190839.0933
82.3076-0.41491.18950.10050.08024.0484-0.0179-0.1425-0.09950.0064-0.00910.030.0077-0.31750.02710.08460.01370.00980.1698-0.01580.1202-1.883247.027115.6602
91.2061-0.0914-0.37411.0463-0.15450.4362-0.0124-0.0158-0.0039-0.02950.03250.0606-0.00830.018-0.02010.08190.0119-0.00570.1298-0.0090.09649.894542.447811.132
100.5661-0.29650.13842.0055-0.30161.505-0.0249-0.0845-0.02350.0184-0.0089-0.0698-0.0601-0.07310.03380.0409-0.01190.01570.13430.00760.091424.451243.4129-1.5665
112.5980.5451.14791.13940.28331.1228-0.03640.0506-0.1330.13190.0579-0.1554-0.0138-0.0136-0.02160.0919-0.00620.00360.0863-0.00160.130718.990513.3387-1.779
121.0058-0.35620.02243.3381-0.57080.8143-0.00090.0308-0.0108-0.10.05960.0149-0.0099-0.1127-0.05870.0579-0.0073-0.00060.125-0.01180.083920.761941.79150.1965
132.2258-1.52751.2985.1784-0.18451.3360.24490.3085-0.2144-0.6623-0.236700.09290.1019-0.00820.16830.02090.01360.1474-0.03940.109526.273137.2199-8.9777
143.62983.2514-0.95954.9513-0.25570.4478-0.23720.1623-0.1097-0.3640.15810.11090.0055-0.00450.07910.16050.00610.00120.11210.00770.043215.127123.0142-6.6403
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 - 296
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 - 298

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