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- PDB-4de4: Crystal structure of aminoglycoside phosphotransferase APH(2")-Id... -

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Basic information

Entry
Database: PDB / ID: 4de4
TitleCrystal structure of aminoglycoside phosphotransferase APH(2")-Id/APH(2")-IVa in complex with HEPES
ComponentsAPH(2")-Id
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID / NIAID / National Institute of Allergy and Infectious Diseases / EUKARYOTIC PROTEIN KINASE-LIKE FOLD / AMINOGLYCOSIDE PHOSPHOTRANSFERASE / KINASE / AMINOGLYCOSIDES / INTRACELLULAR
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
Biological speciesEnterococcus casseliflavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsStogios, P.J. / Minasov, G. / Tan, K. / Nocek, B. / Evdokimova, E. / Egorova, O. / Di Leo, R. / Li, H. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Chem.Biol. / Year: 2011
Title: A small molecule discrimination map of the antibiotic resistance kinome.
Authors: Shakya, T. / Stogios, P.J. / Waglechner, N. / Evdokimova, E. / Ejim, L. / Blanchard, J.E. / McArthur, A.G. / Savchenko, A. / Wright, G.D.
History
DepositionJan 19, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 8, 2012ID: 3R80
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name

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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)77,0354
Polymers76,5582
Non-polymers4772
Water4,864270
1
A: APH(2")-Id
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5172
Polymers38,2791
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: APH(2")-Id
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5172
Polymers38,2791
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.541, 101.214, 71.166
Angle α, β, γ (deg.)90.00, 97.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein APH(2")-Id / APH(2")-IVa


Mass: 38279.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus casseliflavus (bacteria) / Gene: aph(2")-Id / Plasmid: P15TV LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O68183
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 1.98 Å3/Da / Density % sol: 38.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M NASCN, 20% PEG3350, 2 MM GTP, 2.5 MM GENTAMICIN, PH 7.5, 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: Aug 5, 2009
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 39540 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rsym value: 0.059 / Net I/σ(I): 35.71
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3.11 / Rsym value: 0.388 / % possible all: 97.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.autosol)model building
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2→28.988 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0.1 / Phase error: 29.55 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2722 1999 5.17 %random
Rwork0.2217 ---
obs0.2243 38669 95.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.649 Å2 / ksol: 0.351 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-11.9955 Å20 Å21.7516 Å2
2---4.2162 Å20 Å2
3---1.4913 Å2
Refinement stepCycle: LAST / Resolution: 2→28.988 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4924 0 30 270 5224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025088
X-RAY DIFFRACTIONf_angle_d0.5996860
X-RAY DIFFRACTIONf_dihedral_angle_d11.4481956
X-RAY DIFFRACTIONf_chiral_restr0.043720
X-RAY DIFFRACTIONf_plane_restr0.003881
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.07150.36031900.3183478X-RAY DIFFRACTION92
2.0715-2.15440.33911950.29013584X-RAY DIFFRACTION94
2.1544-2.25240.29541980.26623615X-RAY DIFFRACTION95
2.2524-2.37110.30951990.26043653X-RAY DIFFRACTION96
2.3711-2.51960.28831980.24183635X-RAY DIFFRACTION96
2.5196-2.7140.2782020.2533703X-RAY DIFFRACTION97
2.714-2.98680.30372030.24423741X-RAY DIFFRACTION98
2.9868-3.41850.28152060.22323767X-RAY DIFFRACTION99
3.4185-4.30460.25412080.19083817X-RAY DIFFRACTION99
4.3046-28.99110.23382000.19243677X-RAY DIFFRACTION95
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)
11.81940.34740.74134.27881.07132.9905-0.0137-0.0198-0.07650.12740.1233-0.51610.79690.7744-0.10910.44710.20440.09770.36530.04150.224912.500615.405416.0045
22.49410.1565-0.86153.31980.35662.06280.08520.21090.2569-0.1321-0.1868-0.4905-0.26460.10380.11580.19350.0305-0.05640.22080.16340.26549.45147.820523.2011
30.9358-0.12330.24374.98620.60052.05840.00840.08580.0832-0.5644-0.10230.168-0.25760.05020.00630.45570.1376-0.01340.0415-0.02010.09141.732827.8089-2.8448
40.5797-1.23830.31637.42420.07810.899-0.0961-0.129-0.02170.36450.10350.29910.1116-0.1328-0.00460.1734-0.02790.01380.2268-0.04130.1442-4.097534.222639.0345
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 1:99
2X-RAY DIFFRACTION2chain B and resid 1:99
3X-RAY DIFFRACTION3chain A and resid 100:296
4X-RAY DIFFRACTION4chain B and resid 100:298

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