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- PDB-4pdy: Crystal structure of aminoglycoside phosphotransferase from Alicy... -

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Basic information

Entry
Database: PDB / ID: 4pdy
TitleCrystal structure of aminoglycoside phosphotransferase from Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446
ComponentsAminoglycoside phosphotransferase
KeywordsTRANSFERASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / aminoglycoside phosphotransferase
Function / homology
Function and homology information


transferase activity
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
HISTIDINE / THIOCYANATE ION / Aminoglycoside phosphotransferase
Similarity search - Component
Biological speciesAlicyclobacillus acidocaldarius subsp. acidocaldarius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.35 Å
AuthorsChang, C. / Li, H. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be published
Title: Crystal structure of aminoglycoside phosphotransferase from Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446
Authors: Chang, C. / Li, H. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionApr 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Derived calculations
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / software / struct_keywords
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _struct_keywords.text
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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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)41,27110
Polymers40,6501
Non-polymers6219
Water6,485360
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.522, 51.955, 145.851
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Aminoglycoside phosphotransferase


Mass: 40649.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alicyclobacillus acidocaldarius subsp. acidocaldarius (bacteria)
Strain: DSM 446 / Gene: Aaci_0449 / Plasmid: pMCSG57 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: C8WS74
#2: Chemical ChemComp-HIS / HISTIDINE / Histidine


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10N3O2
#3: Chemical
ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CNS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 1.75 Å3/Da / Density % sol: 29.66 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.5M potassium thiocyanate, 1.0M sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 18, 2012
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. all: 63763 / Num. obs: 63586 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Rmerge(I) obs: 0.067 / Χ2: 1.7 / Net I/av σ(I): 38.776 / Net I/σ(I): 10.4 / Num. measured all: 436171
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.35-1.364.50.53515330.85296.5
1.36-1.374.80.55915100.88598.1
1.37-1.395.40.53215800.8499.3
1.39-1.45.90.52415750.887100
1.4-1.416.20.52215200.844100
1.41-1.436.60.45116130.831100
1.43-1.447.10.43615720.844100
1.44-1.457.10.40915670.854100
1.45-1.477.10.35715480.86100
1.47-1.497.10.34115910.896100
1.49-1.57.10.31915730.903100
1.5-1.527.20.27315800.954100
1.52-1.547.20.26315440.979100
1.54-1.567.20.22816040.985100
1.56-1.587.20.21915741.014100
1.58-1.67.20.20615701.051100
1.6-1.627.20.18515991.094100
1.62-1.657.20.17515521.112100
1.65-1.677.20.1615761.153100
1.67-1.77.20.14715811.212100
1.7-1.737.20.1415861.254100
1.73-1.767.20.13215671.31100
1.76-1.87.20.11716041.397100
1.8-1.837.20.11115651.502100
1.83-1.877.20.09916071.518100
1.87-1.927.20.09415671.691100
1.92-1.967.20.08716021.775100
1.96-2.027.20.07915851.893100
2.02-2.087.20.07216121.978100
2.08-2.147.20.06815662.159100
2.14-2.227.10.06716262.366100
2.22-2.317.10.06615882.641100
2.31-2.417.10.06615992.901100
2.41-2.547.10.06816263.252100
2.54-2.770.06416233.33100
2.7-2.9170.05816333.333100
2.91-3.26.80.0516263.083100
3.2-3.666.60.04216443.06999.8
3.66-4.626.70.03916753.27499.7
4.62-506.30.04517234.01895.9

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.35→29.86 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.261 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.056
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1736 3220 5.1 %RANDOM
Rwork0.1309 60268 --
obs0.133 63488 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 83.71 Å2 / Biso mean: 17.878 Å2 / Biso min: 7.91 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å20 Å2
2---1.86 Å2-0 Å2
3---2.56 Å2
Refinement stepCycle: final / Resolution: 1.35→29.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2702 0 24 360 3086
Biso mean--22.77 31.87 -
Num. residues----333
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192989
X-RAY DIFFRACTIONr_bond_other_d0.0010.022746
X-RAY DIFFRACTIONr_angle_refined_deg1.291.9284064
X-RAY DIFFRACTIONr_angle_other_deg0.7836267
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0125367
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.16322.229166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.52615462
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4451537
X-RAY DIFFRACTIONr_chiral_restr0.0830.2413
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213538
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02817
X-RAY DIFFRACTIONr_rigid_bond_restr2.43735735
X-RAY DIFFRACTIONr_sphericity_free31.717583
X-RAY DIFFRACTIONr_sphericity_bonded11.3255928
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 254 -
Rwork0.23 4215 -
all-4469 -
obs--95.86 %

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