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- PDB-4dtb: Crystal Structure of F95Y Aminoglycoside-2''-Phosphotransferase T... -

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Basic information

Entry
Database: PDB / ID: 4dtb
TitleCrystal Structure of F95Y 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 / FOURIER SYNTHESIS / 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)73,6275
Polymers73,0252
Non-polymers6023
Water3,549197
1
A: APH(2'')-Id
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8313
Polymers36,5131
Non-polymers3192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: APH(2'')-Id
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7962
Polymers36,5131
Non-polymers2831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-9 kcal/mol
Surface area28120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.272, 101.341, 73.600
Angle α, β, γ (deg.)90.00, 100.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 36512.551 Da / Num. of mol.: 2 / Mutation: F95Y
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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / 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: 2.12 Å3/Da / Density % sol: 42.03 %
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: Jan 16, 2012
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: 35847 / Num. obs: 35596 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 7.3 % / Rsym value: 0.086 / Net I/σ(I): 23.5
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 4.7 / Rsym value: 0.31 / % possible all: 91.2

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.921 / SU B: 12.068 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R: 0.259 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24998 1783 5 %RANDOM
Rwork0.1971 ---
all0.19977 33783 --
obs0.19977 33783 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.676 Å2
Baniso -1Baniso -2Baniso -3
1-1.73 Å20 Å2-0.89 Å2
2---1.83 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4800 0 41 197 5038
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0225012
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8891.976800
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.425607
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.26624.96248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.27915865
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6511517
X-RAY DIFFRACTIONr_chiral_restr0.1290.2730
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213843
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_it0.9461.52988
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.71324843
X-RAY DIFFRACTIONr_scbond_it3.10532024
X-RAY DIFFRACTIONr_scangle_it4.7474.51950
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 124 -
Rwork0.226 2247 -
obs--91.16 %
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)
16.68287.5784.615411.50381.51359.4551-0.38151.21231.0902-1.13580.42062.32660.5838-0.9918-0.0390.1757-0.1921-0.18130.49920.19120.5041-4.08998.32212.1205
21.3086-0.50140.73181.3869-0.92571.4760.0280.0141-0.02960.01130.02380.23630.1465-0.0195-0.05180.2348-0.01020.0180.16590.00980.18946.177411.266520.6567
30.9024-0.10710.00221.7387-0.58121.74970.0658-0.0714-0.0451-0.0517-0.0317-0.118-0.05830.0286-0.03410.18390.01910.0350.16310.00460.142315.08768.224438.0729
41.6117-1.2485-0.6443.35060.70380.9038-0.0190.0042-0.04050.02510.046-0.2050.0748-0.163-0.0270.2587-0.03860.00830.1445-0.00850.200813.697539.320136.6315
51.38430.77510.31744.5772-0.81471.532-0.0303-0.0169-0.0222-0.03780.06930.0009-0.094-0.058-0.0390.22790.00770.0170.16390.01040.144712.595511.015234.3132
62.01470.30720.64263.8872-1.09032.48540.0174-0.33620.21650.1628-0.02960.126-0.1699-0.13610.01210.2929-0.0013-0.01660.1663-0.01650.135615.24214.749445.0807
73.921-2.61881.23015.7343-1.68240.63860.013-0.10210.0040.13490.20910.47530.097-0.0586-0.22220.3003-0.03410.04930.13840.02320.19457.475929.715838.8617
83.2259-0.330.7669-0.463-0.44714.06730.0336-0.0655-0.11240.0534-0.01650.06270.0998-0.1869-0.0170.17580.03040.00420.1937-0.01680.1834-1.874746.548815.4614
91.8719-0.1622-0.28711.3409-0.15960.520.0198-0.0311-0.051-0.03990.01130.066-0.01020.0109-0.03110.17970.0037-0.00630.1735-0.010.155310.124842.219111.0728
101.2517-0.34860.42622.4382-0.39781.61830.00510.01210.01910.0426-0.0611-0.1378-0.1314-0.0520.0560.13390.00620.01310.1740.01040.14524.451443.0198-1.8151
113.01781.36761.17951.60790.69140.94790.0628-0.0317-0.24950.12580.0457-0.1979-0.0436-0.0122-0.10850.1861-0.0061-0.00730.15270.00850.215219.007412.9839-1.8689
121.0771-0.47540.06443.642-0.88681.37950.02450.0821-0.0576-0.08640.0030.0290.0057-0.1046-0.02750.1558-0.002-0.00630.1863-0.01580.162720.627941.24720.2632
134.0065-1.4971.32075.0323-0.57681.99040.20110.4078-0.2361-0.5425-0.1623-0.04780.13940.1026-0.03870.22220.0280.02960.1941-0.03030.145426.265336.7912-8.838
147.11523.7969-1.34284.1153-0.6016-0.1186-0.07760.11150.1691-0.1590.13250.196-0.05220.0175-0.05490.30250.02040.00350.172-0.00010.145415.198622.9045-6.1606
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 - 297

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