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- PDB-3dfk: The crystal structure of teicoplanin pseudoaglycone deacetylase O... -

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Basic information

Entry
Database: PDB / ID: 3dfk
TitleThe crystal structure of teicoplanin pseudoaglycone deacetylase Orf2* bound to one of its products decanoic acid
ComponentsTeicoplanin pseudoaglycone deacetylase Orf2
KeywordsHYDROLASE / bound to decanoic acid / alpha-beta single domain
Function / homology
Function and homology information


glycoside metabolic process / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / acyltransferase activity / ligase activity / glycosyltransferase activity / metal ion binding
Similarity search - Function
LmbE-like / N-acetylglucosaminyl phosphatidylinositol deacetylase-related / Putative deacetylase LmbE-like domain superfamily / GlcNAc-PI de-N-acetylase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DECANOIC ACID / LmbE family N-acetylglucosaminyl deacetylase
Similarity search - Component
Biological speciesActinoplanes teichomyceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsZou, Y. / Brunzelle, J.S. / Nair, S.K.
CitationJournal: Chem.Biol. / Year: 2008
Title: Crystal structures of lipoglycopeptide antibiotic deacetylases: implications for the biosynthesis of a40926 and teicoplanin.
Authors: Zou, Y. / Brunzelle, J.S. / Nair, S.K.
History
DepositionJun 12, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Teicoplanin pseudoaglycone deacetylase Orf2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5333
Polymers30,2951
Non-polymers2382
Water4,522251
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.530, 64.263, 50.375
Angle α, β, γ (deg.)90.00, 99.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Teicoplanin pseudoaglycone deacetylase Orf2


Mass: 30295.033 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinoplanes teichomyceticus (bacteria)
Gene: tcp14 / References: UniProt: Q6ZZJ1
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-DKA / DECANOIC ACID


Mass: 172.265 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H20O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.87 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9704
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9704 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. obs: 22587

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→25 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.261 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22009 1219 5.1 %RANDOM
Rwork0.17628 ---
obs0.17859 22587 97.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.144 Å2
Baniso -1Baniso -2Baniso -3
1-1.51 Å20 Å2-0.76 Å2
2---1.05 Å20 Å2
3----0.7 Å2
Refinement stepCycle: LAST / Resolution: 1.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2074 0 13 251 2338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212136
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1791.9442905
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.95265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.14123.486109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.61315324
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5041519
X-RAY DIFFRACTIONr_chiral_restr0.0820.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021684
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.21040
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21467
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2211
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0030.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1380.232
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1180.230
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8351.51345
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.49122127
X-RAY DIFFRACTIONr_scbond_it2.4283868
X-RAY DIFFRACTIONr_scangle_it3.7294.5778
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 102 -
Rwork0.17 1622 -
obs--97.02 %

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