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- PDB-4dfb: Crystal structure of aminoglycoside phosphotransferase aph(2")-id... -

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Basic information

Entry
Database: PDB / ID: 4dfb
TitleCrystal structure of aminoglycoside phosphotransferase aph(2")-id/aph(2")-iva in complex with kanamycin
ComponentsAPH(2")-Id
KeywordsTRANSFERASE/ANTIBIOTIC / STRUCTURAL GENOMICS / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID / EUKARYOTIC PROTEIN KINASE-LIKE FOLD / AMINOGLYCOSIDE PHOSPHOTRANSFERASE / KINASE / TRANSFERASE / AMINOGLYCOSIDES / KANAMYCIN / ANTIBIOTIC / TRANSFERASE-ANTIBIOTIC complex
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
KANAMYCIN A / APH(2'')-Id
Similarity search - Component
Biological speciesEnterococcus casseliflavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsStogios, P.J. / Minasov, G. / Osipiuk, J. / Evdokimova, E. / Egorova, E. / 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 23, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 8, 2012ID: 3R81
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2012Group: Database references
Revision 1.2Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_nat / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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)77,5986
Polymers76,5582
Non-polymers1,0404
Water8,161453
1
A: APH(2")-Id
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7993
Polymers38,2791
Non-polymers5202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: APH(2")-Id
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7993
Polymers38,2791
Non-polymers5202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.669, 101.153, 71.701
Angle α, β, γ (deg.)90.00, 98.33, 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-KAN / KANAMYCIN A


Mass: 484.499 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H36N4O11 / Comment: antibiotic*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 453 / 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 Å3/Da / Density % sol: 38.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M NACL, 0.1 M HEPES PH 7.5, 29% PEG3350, 1 MM KANAMYCIN, 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: Oct 6, 2009
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 43687 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Rsym value: 0.066 / Net I/σ(I): 33.73
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 3.21 / Rsym value: 0.459 / % possible all: 98.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.solve)model building
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→34.17 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 0.1 / Phase error: 28.15 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2584 2000 4.68 %random
Rwork0.2058 ---
obs0.2083 42711 97.45 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.827 Å2 / ksol: 0.372 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-21.9999 Å20 Å23.5159 Å2
2--9.8115 Å2-0 Å2
3---20.7181 Å2
Refinement stepCycle: LAST / Resolution: 1.95→34.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4957 0 68 453 5478
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035203
X-RAY DIFFRACTIONf_angle_d0.7417029
X-RAY DIFFRACTIONf_dihedral_angle_d11.5862027
X-RAY DIFFRACTIONf_chiral_restr0.045762
X-RAY DIFFRACTIONf_plane_restr0.003894
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.01970.30171880.26543841X-RAY DIFFRACTION93
2.0197-2.10060.34111950.25863953X-RAY DIFFRACTION95
2.1006-2.19620.291970.24144019X-RAY DIFFRACTION97
2.1962-2.31190.30711990.2264052X-RAY DIFFRACTION97
2.3119-2.45670.28272020.2354087X-RAY DIFFRACTION98
2.4567-2.64630.32572020.23774138X-RAY DIFFRACTION99
2.6463-2.91250.34232040.24284125X-RAY DIFFRACTION99
2.9125-3.33370.27732050.20994186X-RAY DIFFRACTION100
3.3337-4.19890.20022050.17154192X-RAY DIFFRACTION100
4.1989-34.17520.20732030.17314118X-RAY DIFFRACTION97
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)
10.16840.05660.01480.1453-0.02660.1182-0.00280.0068-0.00960.0056-0.0207-0.0567-0.01070.0337-0.013-0.0265-0.0104-0.0810.04740.05870.02078.948572.884323.4333
20.8743-0.08670.14230.84570.40370.7831-0.0031-0.0159-0.0191-0.02960.05-0.26520.11390.1765-0.08750.13070.09530.11120.04980.01480.151212.21940.866616.2197
30.2057-0.0723-0.0190.52350.09050.10780.0446-0.0783-0.0520.1471-0.020.08710.03340.02790.01320.0356-0.00520.0120.0238-0.00260.0231-4.524759.493339.3451
40.042-0.0149-0.00130.31270.0930.09390.01830.06110.0197-0.014-0.04270.0529-0.04560.0184-0.05160.22970.14910.1007-0.1407-0.1359-0.08671.738453.6628-2.8946
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 100:299
4X-RAY DIFFRACTION4chain B and resid 100:301

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