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- PDB-4lei: Spinosyn Forosaminyltransferase SpnP -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4lei
TitleSpinosyn Forosaminyltransferase SpnP
ComponentsNDP-forosamyltransferase
KeywordsTRANSFERASE / Glycosyltransferase
Function / homology
Function and homology information


UDP-glycosyltransferase activity / hexosyltransferase activity / antibiotic biosynthetic process
Similarity search - Function
Glycosyltransferase, activator-dependent family / : / Erythromycin biosynthesis protein CIII-like, N-terminal domain / Erythromycin biosynthesis protein CIII-like, central / : / Erythromycin biosynthesis protein CIII-like, C-terminal domain / UDP-glucuronosyl/UDP-glucosyltransferase / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
THYMIDINE-5'-DIPHOSPHATE / Probable NDP-forosamyltransferase
Similarity search - Component
Biological speciesSaccharopolyspora spinosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsIsiorho, E.A. / Liu, H.-W. / Keatinge-Clay, A.K.
CitationJournal: Biochemistry / Year: 2014
Title: Structural studies of the spinosyn forosaminyltransferase, SpnP.
Authors: Isiorho, E.A. / Jeon, B.S. / Kim, N.H. / Liu, H.W. / Keatinge-Clay, A.T.
History
DepositionJun 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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: NDP-forosamyltransferase
B: NDP-forosamyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,8094
Polymers101,0042
Non-polymers8042
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-6 kcal/mol
Surface area30890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.369, 162.369, 81.279
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein NDP-forosamyltransferase


Mass: 50502.125 Da / Num. of mol.: 2 / Fragment: UNP residues 17-455
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharopolyspora spinosa (bacteria) / Gene: spnP / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ALN7
#2: Chemical ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE


Mass: 402.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.62 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 4.24
Details: 7 mM PSA, 46% (w/v) PEG 200, 0.6-3.0% (w/v) dextran sulfate MR 5,000, 0.2 M sodium chloride, 0.1 M phosphate citrate buffer, pH 4.24 , VAPOR DIFFUSION, SITTING DROP, temperature 298.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 27, 2013
RadiationMonochromator: Asymmetric cut single crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.15→114.81 Å / Num. all: 19214 / Num. obs: 18175 / % possible obs: 99.02 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.15→3.231 Å / % possible all: 95.25

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERMRphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.15→114.81 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.809 / SU B: 24.83 / SU ML: 0.433 / Cross valid method: THROUGHOUT / ESU R Free: 0.577 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.31368 985 5.1 %RANDOM
Rwork0.20891 ---
all0.21403 19214 --
obs0.21403 18175 99.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.668 Å2
Baniso -1Baniso -2Baniso -3
1-3.79 Å20 Å20 Å2
2--3.79 Å20 Å2
3----7.59 Å2
Refinement stepCycle: LAST / Resolution: 3.15→114.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5827 0 50 81 5958
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196004
X-RAY DIFFRACTIONr_bond_other_d0.0030.0226
X-RAY DIFFRACTIONr_angle_refined_deg1.8141.9868193
X-RAY DIFFRACTIONr_angle_other_deg1.01360
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3595740
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.32823.015262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.68815976
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7521560
X-RAY DIFFRACTIONr_chiral_restr0.1090.2946
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214531
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.15→3.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 70 -
Rwork0.257 1134 -
obs--95.25 %

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