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- PDB-3uyk: Spinosyn Rhamnosyltransferase SpnG complexed with spinosyn aglycone -

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Basic information

Entry
Database: PDB / ID: 3uyk
TitleSpinosyn Rhamnosyltransferase SpnG complexed with spinosyn aglycone
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, 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
Chem-0CX / beta-D-glucopyranose / Probable NDP-rhamnosyltransferase
Similarity search - Component
Biological speciesSaccharopolyspora spinosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)82,4945
Polymers81,8872
Non-polymers6073
Water9,188510
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-21 kcal/mol
Surface area27800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.021, 57.076, 68.100
Angle α, β, γ (deg.)81.98, 74.10, 86.07
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-0CX / (2R,3aS,5aR,5bS,9S,13S,14R,16aS,16bR)-9-ethyl-2,13-dihydroxy-14-methyl-2,3,3a,5a,5b,6,9,10,11,12,13,14,16a,16b-tetradecahydro-1H-as-indaceno[3,2-d]oxacyclododecine-7,15-dione


Mass: 402.524 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H34O5
#4: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


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


Mass: 18.015 Da / Num. of mol.: 510 / 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: 2.44 Å3/Da / Density % sol: 49.6 %
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: 1.7→29.83 Å / Num. all: 84558 / Num. obs: 78024 / % possible obs: 96.92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.7→1.75 Å / % possible all: 91.99

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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

3tsa


Resolution: 1.7→29.83 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.929 / SU B: 2.175 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23431 4101 5 %RANDOM
Rwork0.18887 ---
all0.19113 84558 --
obs0.19113 78024 96.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.326 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20.01 Å2-0.01 Å2
2---0.01 Å20.01 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5527 0 42 510 6079
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0195710
X-RAY DIFFRACTIONr_bond_other_d0.0020.0234
X-RAY DIFFRACTIONr_angle_refined_deg2.2561.9867840
X-RAY DIFFRACTIONr_angle_other_deg1.282382
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5125738
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.4823.348224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.20415811
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2461543
X-RAY DIFFRACTIONr_chiral_restr0.1610.2921
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0224402
X-RAY DIFFRACTIONr_gen_planes_other0.0050.026
LS refinement shellResolution: 1.7→1.747 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 259 -
Rwork0.283 5481 -
obs--91.99 %

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