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- PDB-4dbx: Crystal structure of aminoglycoside phosphotransferase APH(2")-ID... -

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Basic information

Entry
Database: PDB / ID: 4dbx
TitleCrystal structure of aminoglycoside phosphotransferase APH(2")-ID/APH(2")-IVA
ComponentsAPH(2")-ID
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / MCSG / Midwest Center for Structural Genomics / EUKARYOTIC PROTEIN KINASE-LIKE FOLD / AMINOGLYCOSIDE PHOSPHOTRANSFERASE / KINASE / AMINOGLYCOSIDES / INTRACELLULAR / PSI-Biology
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: 2.004 Å
AuthorsStogios, P.J. / Minasov, G. / Tan, K. / Nocek, B. / Singer, A.U. / Evdokimova, E. / Egorova, E. / Di Leo, R. / Li, H. / Shakya, T. ...Stogios, P.J. / Minasov, G. / Tan, K. / Nocek, B. / Singer, A.U. / Evdokimova, E. / Egorova, E. / Di Leo, R. / Li, H. / Shakya, T. / Wright, G.D. / Savchenko, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
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 16, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 1, 2012ID: 3R7Z
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2012Group: Other
Revision 1.2Apr 25, 2012Group: Other / Structure summary
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: APH(2")-ID


Theoretical massNumber of molelcules
Total (without water)38,2791
Polymers38,2791
Non-polymers00
Water5,405300
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.583, 63.177, 103.456
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 38279.039 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.42 Å3/Da / Density % sol: 49.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, 10% PEG 6K, 5% MPD, 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 9, 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: 25489 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7 % / Rsym value: 0.088 / Net I/σ(I): 34.04
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 5.13 / Rsym value: 0.508 / % possible all: 96.3

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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: 2.004→30.269 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1274 5.04 %random
Rwork0.185 ---
obs0.1872 25284 98.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.226 Å2 / ksol: 0.319 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.5816 Å20 Å20 Å2
2--2.2795 Å2-0 Å2
3---2.6968 Å2
Refinement stepCycle: LAST / Resolution: 2.004→30.269 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2447 0 0 300 2747
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052517
X-RAY DIFFRACTIONf_angle_d0.9033396
X-RAY DIFFRACTIONf_dihedral_angle_d13.216960
X-RAY DIFFRACTIONf_chiral_restr0.063358
X-RAY DIFFRACTIONf_plane_restr0.004440
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0042-2.08440.28171220.2482501X-RAY DIFFRACTION94
2.0844-2.17930.26561550.21822604X-RAY DIFFRACTION98
2.1793-2.29410.20891180.19752630X-RAY DIFFRACTION99
2.2941-2.43780.24991440.1852664X-RAY DIFFRACTION99
2.4378-2.62590.27591450.19632655X-RAY DIFFRACTION100
2.6259-2.890.24241390.19782681X-RAY DIFFRACTION100
2.89-3.30770.23131580.1862687X-RAY DIFFRACTION100
3.3077-4.16570.21331440.16882735X-RAY DIFFRACTION100
4.1657-30.27290.20771490.17352853X-RAY DIFFRACTION99
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)
11.66980.6262-0.18142.18071.25045.4767-0.02290.13020.0994-0.23410.03870.1165-0.2839-0.31030.0110.18330.0020.02540.14310.04280.14333.857336.194613.5781
20.6821-0.5499-0.37731.26140.30431.28190.0150.1066-0.0963-0.0283-0.09560.27660.0216-0.2539-0.005-0.0452-0.0139-0.0083-0.0354-0.0467-0.005623.957336.28336.895
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 2:99
2X-RAY DIFFRACTION2chain A and resid 100:296

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