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- PDB-3uyl: Spinosyn Rhamnosyltransferase SpnG complexed with thymidine dipho... -

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Basic information

Entry
Database: PDB / ID: 3uyl
TitleSpinosyn Rhamnosyltransferase SpnG complexed with thymidine diphosphate
ComponentsNDP-rhamnosyltransferase
KeywordsTRANSFERASE / Glycosyltransferase
Function / homology
Function and homology information


UDP-glycosyltransferase activity / hexosyltransferase activity / antibiotic biosynthetic process
Similarity search - Function
Erythromycin biosynthesis protein CIII-like, central / Protein of unknown function (DUF1205) / UDP-glucuronosyl/UDP-glucosyltransferase / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-D-glucopyranose / THYMIDINE-5'-DIPHOSPHATE / Probable NDP-rhamnosyltransferase
Similarity search - Component
Biological speciesSaccharopolyspora spinosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsIsiorho, E.A. / Liu, H.-W. / Keatinge-Clay, A.T.
CitationJournal: Biochemistry / Year: 2012
Title: Structural Studies of the Spinosyn Rhamnosyltransferase, SpnG.
Authors: Isiorho, E.A. / Liu, H.W. / Keatinge-Clay, A.T.
History
DepositionDec 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 29, 2012Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NDP-rhamnosyltransferase
B: NDP-rhamnosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,9207
Polymers81,8872
Non-polymers1,0335
Water7,512417
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-58 kcal/mol
Surface area27150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.152, 57.629, 68.203
Angle α, β, γ (deg.)81.63, 73.79, 85.74
Int Tables number1
Space group name H-MP1

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Components

#1: Protein NDP-rhamnosyltransferase / SpnG


Mass: 40943.582 Da / Num. of mol.: 2 / Fragment: UNP residues 1-386
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharopolyspora spinosa (bacteria) / Gene: spnG / Production host: Escherichia coli (E. coli)
References: UniProt: Q9ALM8, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE / Thymidine diphosphate


Mass: 402.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Sugar ChemComp-GLC / alpha-D-glucopyranose / Glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 417 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE AUTHORS STATE THAT RESIDUE ALA 360 IS CORRECT.

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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: 2.47 Å3/Da / Density % sol: 50.16 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 18% w/v PEG3350, 12.5-13.5% w/v glucose, 1% v/v glycerol, 0.1 M magnesium formate, 0.1 M sodium cacodylate, pH 6.9, 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: Jul 10, 2010
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: 1.85→24.62 Å / Num. all: 66093 / Num. obs: 57920 / % possible obs: 92.02 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.85→1.9 Å / % possible all: 88.56

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERMRphasing
REFMACversion: 5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3TSA
Resolution: 1.85→24.62 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.84 / SU B: 5.337 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.29137 3104 5.1 %RANDOM
Rwork0.23154 ---
obs0.2346 57920 92.02 %-
all-66093 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.176 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0.01 Å2-0.01 Å2
2--0 Å20.01 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.85→24.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5533 0 64 417 6014
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0195736
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212
X-RAY DIFFRACTIONr_angle_refined_deg2.1411.9917880
X-RAY DIFFRACTIONr_angle_other_deg1.886320
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6165738
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.25723.289225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.54415814
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6581544
X-RAY DIFFRACTIONr_chiral_restr0.1340.2918
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0224406
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024
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_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.855→1.903 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.455 219 -
Rwork0.419 4076 -
obs--88.56 %

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