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- PDB-4dca: Crystal structure of aminoglycoside phosphotransferase APH(2'')-I... -

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Basic information

Entry
Database: PDB / ID: 4dca
TitleCrystal structure of aminoglycoside phosphotransferase APH(2'')-Ib, ADP-bound
ComponentsAminoglycoside phosphotransferase
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID / EUKARYOTIC PROTEIN KINASE-LIKE FOLD / AMINOGLYCOSIDE PHOSPHOTRANSFERASE / KINASE / ANTIBIOTIC RESISTANCE / AMINOGLYCOSIDES / INTRACELLULAR
Function / homology
Function and homology information


transferase activity / 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-5'-DIPHOSPHATE / Aminoglycoside phosphotransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsStogios, P.J. / Minasov, G. / Singer, A.U. / Tan, K. / Nocek, B. / Evdokimova, E. / Egorova, O. / Di Leo, R. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of aminoglycoside phosphotransferase APH(2'')-Ib, ADP-bound
Authors: Stogios, P.J. / Minasov, G. / Singer, A.U. / Tan, K. / Nocek, B. / Evdokimova, E. / Egorova, O. / Di Leo, R. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJan 17, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 1, 2012ID: 3R70
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aminoglycoside phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6073
Polymers38,1551
Non-polymers4522
Water6,233346
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.938, 88.465, 62.299
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-705-

HOH

21A-830-

HOH

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Components

#1: Protein Aminoglycoside phosphotransferase


Mass: 38155.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: aph(2')-Ib / Plasmid: P15TV LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q93ET9
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 2.34 Å3/Da / Density % sol: 47.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M MG CHLORIDE, 0.1 M BIS-TRIS PH 6.5, 25% PEG3350, 2.5 MM ATP, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 16, 2009
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 33721 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Rsym value: 0.047 / Net I/σ(I): 36.09
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 5 % / Mean I/σ(I) obs: 2.23 / Rsym value: 0.694 / % possible all: 99

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.8→29.381 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.46 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2246 1607 5.01 %random
Rwork0.1954 ---
obs0.1969 32074 94.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.76 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.5802 Å2-0 Å2-0 Å2
2---9.5672 Å20 Å2
3----9.0155 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.381 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2466 0 28 346 2840
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092592
X-RAY DIFFRACTIONf_angle_d1.1473505
X-RAY DIFFRACTIONf_dihedral_angle_d14.924997
X-RAY DIFFRACTIONf_chiral_restr0.077379
X-RAY DIFFRACTIONf_plane_restr0.004451
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.86490.33311460.28592596X-RAY DIFFRACTION82
1.8649-1.93960.29361380.25012789X-RAY DIFFRACTION88
1.9396-2.02790.26911580.22182909X-RAY DIFFRACTION91
2.0279-2.13470.2521550.213050X-RAY DIFFRACTION96
2.1347-2.26840.22571630.19813095X-RAY DIFFRACTION97
2.2684-2.44350.24311610.20173148X-RAY DIFFRACTION98
2.4435-2.68930.26771720.19783180X-RAY DIFFRACTION99
2.6893-3.0780.23621690.19493222X-RAY DIFFRACTION100
3.078-3.87660.21131690.17453256X-RAY DIFFRACTION100
3.8766-29.38520.18941760.19193222X-RAY DIFFRACTION94
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)
13.05960.1121-2.45323.93540.56133.2242-0.1391-0.3011-0.42240.1212-0.068-0.36430.52030.35920.19090.4370.0707-0.08990.3641-0.00980.2828.544111.070712.5758
20.6519-0.15880.33881.6251-0.52992.40390.0904-0.10820.03260.0539-0.11130.0680.1859-0.1190.01040.2571-0.03210.02220.262-0.03580.2762.833321.060536.2384
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 4:91A - a4 - 91
2X-RAY DIFFRACTION2chain A and resid 92:299A - a92 - 299

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