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- PDB-4m7p: Ensemble refinement of protein crystal structure of macrolide gly... -

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Basic information

Entry
Database: PDB / ID: 4m7p
TitleEnsemble refinement of protein crystal structure of macrolide glycosyltransferases OleD
ComponentsOleandomycin glycosyltransferase
KeywordsTRANSFERASE / Structural Genomics / Protein Structure Initiative / Enzyme Discovery for Natural Product Biosynthesis / NatPro / PSI-Biology
Function / homology
Function and homology information


UDP-glycosyltransferase activity / hexosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases / antibiotic biosynthetic process / response to antibiotic
Similarity search - Function
UDP-glycosyltransferase, MGT-like / Erythromycin biosynthesis protein CIII-like, central / Erythromycin biosynthesis protein CIII-like, C-terminal domain / UDP-glycosyltransferase family, conserved site / UDP-glycosyltransferases signature. / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Oleandomycin glycosyltransferase / Oleandomycin glycosyltransferase
Similarity search - Component
Biological speciesStreptomyces antibioticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.77 Å
AuthorsWang, F. / Helmich, K.E. / Xu, W. / Singh, S. / Olmos Jr., J.L. / Martinez iii, E. / Bingman, C.A. / Thorson, J.S. / Phillips Jr., G.N. / Enzyme Discovery for Natural Product Biosynthesis (NatPro)
CitationJournal: To be Published
Title: Crystal structure of macrolide glycosyltransferases OleD
Authors: Olmos Jr., J.L. / Wang, F. / Martinez iii, E. / Helmich, K.E. / Singh, S. / Xu, W. / Bingman, C.A. / Thorson, J.S. / Phillips Jr., G.N.
History
DepositionAug 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oleandomycin glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9532
Polymers45,9301
Non-polymers231
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)124.134, 124.134, 67.636
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Number of models20
Components on special symmetry positions
IDModelComponents
19A-655-

HOH

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Components

#1: Protein Oleandomycin glycosyltransferase


Mass: 45929.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces antibioticus (bacteria) / Gene: oleD / Production host: Escherichia coli (E. coli) / References: UniProt: Q3HTL6, UniProt: Q53685*PLUS
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.18 Å3/Da / Density % sol: 43.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein Solution (10-15 mg/ml protein, 25mM Tris pH 7.5 and 150mM NaCl) mixed in a 1:1 ratio with the well solution (45% polyacrylate 2100, sodium salt, 0.1M HEPES pH 6.5) Cryoprotected with ...Details: Protein Solution (10-15 mg/ml protein, 25mM Tris pH 7.5 and 150mM NaCl) mixed in a 1:1 ratio with the well solution (45% polyacrylate 2100, sodium salt, 0.1M HEPES pH 6.5) Cryoprotected with 45% polyacrylate 2100, sodium salt, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97939 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 1, 2013
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97939 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. all: 37890 / Num. obs: 37890 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.6 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 9.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine: 1.8.2_1309)model building
PHENIX(phenix.ensemble_refinement: dev_1420)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.8.2_1309phasing
RefinementMethod to determine structure: SAD / Resolution: 1.77→42.081 Å / SU ML: 0.16 / σ(F): 1.3 / Phase error: 20.41 / Stereochemistry target values: ML
Details: AUTHOR MADE THE FOLLOWING COMMENTS: THE ABOUT 10 WATER MOLECULES THAT HAVE 0 B-FACTORS WERE GENERATED AUTOMATICALLY BY PHENIX ENSEMBLE REFINEMENT AND CANNOT BE FURTHER REFINED BY PHENIX ...Details: AUTHOR MADE THE FOLLOWING COMMENTS: THE ABOUT 10 WATER MOLECULES THAT HAVE 0 B-FACTORS WERE GENERATED AUTOMATICALLY BY PHENIX ENSEMBLE REFINEMENT AND CANNOT BE FURTHER REFINED BY PHENIX (BECAUSE PHENIX CURRENTLY DO NOT SUPPORT REGULAR REFINEMENT CONTAINING MULTIPLE MODELS).
RfactorNum. reflection% reflectionSelection details
Rfree0.1884 2004 5.29 %Random
Rwork0.1499 ---
all0.152 37890 --
obs0.152 37890 100 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.77→42.081 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3042 0 1 130 3173
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.016
X-RAY DIFFRACTIONf_angle_d1.867
X-RAY DIFFRACTIONf_dihedral_angle_d18.4
X-RAY DIFFRACTIONf_chiral_restr0.103
X-RAY DIFFRACTIONf_plane_restr0.011
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.81430.30581420.27582562X-RAY DIFFRACTION100
1.8143-1.86330.30391430.22452559X-RAY DIFFRACTION100
1.8633-1.91820.25661420.18662576X-RAY DIFFRACTION100
1.9182-1.98010.23841420.16652564X-RAY DIFFRACTION100
1.9801-2.05090.2221420.15722554X-RAY DIFFRACTION100
2.0509-2.1330.21551460.14892554X-RAY DIFFRACTION100
2.133-2.230.19671430.14182566X-RAY DIFFRACTION100
2.23-2.34760.19961410.14392599X-RAY DIFFRACTION100
2.3476-2.49470.21511420.13932537X-RAY DIFFRACTION100
2.4947-2.68730.19561430.1472570X-RAY DIFFRACTION100
2.6873-2.95760.1681440.14682561X-RAY DIFFRACTION100
2.9576-3.38540.21261470.15162571X-RAY DIFFRACTION100
3.3854-4.26460.15531400.13862553X-RAY DIFFRACTION100
4.2646-42.0930.1681470.14772560X-RAY DIFFRACTION100

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