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- PDB-4ebj: Crystal structure of aminoglycoside 4'-O-adenylyltransferase ANT(... -

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Basic information

Entry
Database: PDB / ID: 4ebj
TitleCrystal structure of aminoglycoside 4'-O-adenylyltransferase ANT(4')-IIb, apo
ComponentsAminoglycoside nucleotidyltransferase
KeywordsTRANSFERASE / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID / NIAID / National Institute of Allergy and Infectious Diseases / Alpha/beta protein / Nucleotidyltransferase (NT) domain / antibiotic resistance / aminoglycoside 4'-O-adenylyltransferase / aminoglycoside antibiotics / tobramycin / amikacin / intracellular
Function / homology
Function and homology information


nucleotidyltransferase activity
Similarity search - Function
Nucleotidyltransferase, substrate binding domain / Nucleotidyltransferase, substrate binding domain / Nucleotidyltransferases domain 2 / Polymerase, nucleotidyl transferase domain / Nucleotidyltransferase domain / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle ...Nucleotidyltransferase, substrate binding domain / Nucleotidyltransferase, substrate binding domain / Nucleotidyltransferases domain 2 / Polymerase, nucleotidyl transferase domain / Nucleotidyltransferase domain / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Aminoglycoside nucleotidyltransferase / Aminoglycoside nucleotidyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsStogios, P.J. / Wawrzak, Z. / Minasov, G. / Evdokimova, E. / Egorova, O. / Yim, V. / Kudritska, M. / Courvalin, P. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal structure of aminoglycoside 4'-O-adenylyltransferase ANT(4')-IIb, apo
Authors: Stogios, P.J. / Wawrzak, Z. / Minasov, G. / Evdokimova, E. / Egorova, O. / Yim, V. / Kudritska, M. / Courvalin, P. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMar 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminoglycoside nucleotidyltransferase
B: Aminoglycoside nucleotidyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,59418
Polymers61,3972
Non-polymers1,19716
Water13,908772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7900 Å2
ΔGint-78 kcal/mol
Surface area22900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.444, 83.482, 90.166
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 Aminoglycoside nucleotidyltransferase


Mass: 30698.689 Da / Num. of mol.: 2 / Fragment: unp residues 2-251
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: BM4530 / Gene: ant(4')-IIb, ant4'-IIb / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q83V96, UniProt: D0E7M2*PLUS
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 772 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THE CORRECT SEQUENCE DOES NOT CONTAIN ANY APPARENT CONFLICT

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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: 2.46 Å3/Da / Density % sol: 49.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M ammonium sulfate, 0.1 M MES, 30% PEG 5K MME, cryoprotectant: 25% ethylene glycol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 5, 2011 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. all: 155176 / Num. obs: 154555 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Rsym value: 0.083 / Net I/σ(I): 27.31
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 2.49 / Rsym value: 0.604 / % possible all: 97.6

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHENIX(phenix.solve)model building
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→28.963 Å / SU ML: 0.18 / σ(F): 0 / Phase error: 17.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1919 3895 5.01 %
Rwork0.1657 --
obs0.167 77704 96.1 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.67 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.5616 Å2-0 Å20 Å2
2---1.625 Å2-0 Å2
3---2.1866 Å2
Refinement stepCycle: LAST / Resolution: 1.6→28.963 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4072 0 70 772 4914
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074373
X-RAY DIFFRACTIONf_angle_d1.0575987
X-RAY DIFFRACTIONf_dihedral_angle_d11.2821634
X-RAY DIFFRACTIONf_chiral_restr0.071674
X-RAY DIFFRACTIONf_plane_restr0.005779
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5986-1.61810.29481220.25142290X-RAY DIFFRACTION84
1.6181-1.63860.29411300.24052386X-RAY DIFFRACTION88
1.6386-1.66020.28411320.22642421X-RAY DIFFRACTION90
1.6602-1.68290.2591360.22012448X-RAY DIFFRACTION91
1.6829-1.70690.25941250.20272476X-RAY DIFFRACTION90
1.7069-1.73240.25791310.19692515X-RAY DIFFRACTION93
1.7324-1.75950.21471330.19122510X-RAY DIFFRACTION93
1.7595-1.78830.20761320.17672549X-RAY DIFFRACTION94
1.7883-1.81920.23331310.17322555X-RAY DIFFRACTION94
1.8192-1.85220.2151380.16462577X-RAY DIFFRACTION95
1.8522-1.88780.17871420.15812600X-RAY DIFFRACTION96
1.8878-1.92640.22521340.16242610X-RAY DIFFRACTION96
1.9264-1.96830.18871420.15852659X-RAY DIFFRACTION97
1.9683-2.0140.18451390.15642670X-RAY DIFFRACTION98
2.014-2.06440.19871380.15562671X-RAY DIFFRACTION98
2.0644-2.12020.18571420.16042686X-RAY DIFFRACTION99
2.1202-2.18250.17951430.15442691X-RAY DIFFRACTION99
2.1825-2.2530.19121410.14762709X-RAY DIFFRACTION99
2.253-2.33350.19431420.15382706X-RAY DIFFRACTION99
2.3335-2.42680.18021430.15332722X-RAY DIFFRACTION99
2.4268-2.53720.21331450.1562740X-RAY DIFFRACTION99
2.5372-2.67090.17821450.15982757X-RAY DIFFRACTION100
2.6709-2.83810.1821440.16222741X-RAY DIFFRACTION100
2.8381-3.0570.20031470.16962768X-RAY DIFFRACTION100
3.057-3.36430.17721470.17082784X-RAY DIFFRACTION100
3.3643-3.85010.17471460.15432790X-RAY DIFFRACTION100
3.8501-4.8470.15811490.1372834X-RAY DIFFRACTION100
4.847-28.96810.17191560.19092944X-RAY DIFFRACTION100
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)
11.95580.65050.6591.5895-0.44241.9922-0.08360.10220.159-0.0020.0325-0.0908-0.1691-0.02820.0090.07910.0572-0.00750.07550.03410.132147.290680.076514.3498
20.5694-0.181-0.03690.7724-0.27660.4323-0.00740.0424-0.007-0.05910.02110.11310.0315-0.0735-0.01790.0475-0.0169-0.00420.0514-0.00240.048651.221854.79731.0443
30.9630.1371-0.44571.36460.22081.0978-0.0098-0.1062-0.12450.10580.0383-0.06980.03510.0141-0.01120.03230.0404-0.00340.0319-0.00690.048769.604736.701726.4106
40.3713-0.1037-0.00110.67460.09430.27750.00620.03720.0987-0.08450.0011-0.0585-0.07680.0683-0.00750.0572-0.0198-0.00210.0480.01130.072868.074266.645924.0175
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resi -8:72
2X-RAY DIFFRACTION2chain A and resi 73:267
3X-RAY DIFFRACTION3chain B and resi -6:72
4X-RAY DIFFRACTION4chain B and resi 73:276

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