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- PDB-4ldp: Spinosyn Forosaminyltransferase SpnP -

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Basic information

Entry
Database: PDB / ID: 4ldp
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
Probable NDP-forosamyltransferase
Similarity search - Component
Biological speciesSaccharopolyspora spinosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsIsiorho, E.A. / Liu, H.-W. / Keatinge-Clay, A.K.
CitationJournal: To be Published
Title: SpnP; Structural Insights into the Activation of GT-1 Glycosyltransferases by Helper Proteins
Authors: Isiorho, E.A. / Jeon, B.-S. / Liu, H.-W. / Keatinge-Clay, A.K.
History
DepositionJun 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NDP-forosamyltransferase
B: NDP-forosamyltransferase


Theoretical massNumber of molelcules
Total (without water)101,0042
Polymers101,0042
Non-polymers00
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-7 kcal/mol
Surface area30110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.421, 162.421, 81.228
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.65 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: 5.0.2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 23, 2012
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: 2.5→46.93 Å / Num. obs: 36239 / % possible obs: 99.65 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.5→2.562 Å / % possible all: 97.31

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERMRphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→46.93 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.922 / SU B: 8.201 / SU ML: 0.185 / Cross valid method: THROUGHOUT / ESU R: 0.344 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25743 1912 5 %RANDOM
Rwork0.20034 ---
all0.20324 71988 --
obs0.20324 36239 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.201 Å2
Baniso -1Baniso -2Baniso -3
1-1.69 Å20 Å20 Å2
2--1.69 Å20 Å2
3----3.37 Å2
Refinement stepCycle: LAST / Resolution: 2.5→46.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5772 0 0 84 5856
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0195895
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9561.9778035
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8155734
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.82623.154260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.39415966
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1771558
X-RAY DIFFRACTIONr_chiral_restr0.1210.2931
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214471
X-RAY DIFFRACTIONr_gen_planes_other
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: 2.5→2.562 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 137 -
Rwork0.266 2578 -
obs--97.31 %

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