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- PDB-3vdm: Crystal Structure of VldE, the pseudo-glycosyltransferase which c... -

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Basic information

Entry
Database: PDB / ID: 3vdm
TitleCrystal Structure of VldE, the pseudo-glycosyltransferase which catalyzes non-glycosidic C-N coupling in Validamycin A biosynthesis
ComponentsVldE
KeywordsTRANSFERASE / Rossmann Fold
Function / homology
Function and homology information


validamine 7-phosphate valienyltransferase / alpha,alpha-trehalose-phosphate synthase (UDP-forming) activity / trehalose biosynthetic process / antibiotic biosynthetic process
Similarity search - Function
Glycosyl transferase, family 20 / Glycosyltransferase family 20 / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Validamine 7-phosphate valienyltransferase
Similarity search - Component
Biological speciesStreptomyces hygroscopicus subsp. limoneus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsCavalier, M.C. / Yim, Y.-S. / Asamizu, S. / Neau, D. / Mahmud, T. / Lee, Y.-H.
CitationJournal: To be Published
Title: Crystal Structure of VldE, the pseudo-glycosyltransferase which catalyzes non-glycosidic C-N coupling in Validamycin A biosynthesis
Authors: Cavalier, M.C. / Yim, Y.-S. / Asamizu, S. / Neau, D. / Mahmud, T. / Lee, Y.-H.
History
DepositionJan 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VldE
B: VldE


Theoretical massNumber of molelcules
Total (without water)110,0132
Polymers110,0132
Non-polymers00
Water8,809489
1
A: VldE

A: VldE


Theoretical massNumber of molelcules
Total (without water)110,0132
Polymers110,0132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area4030 Å2
ΔGint4 kcal/mol
Surface area38310 Å2
MethodPISA
2
B: VldE

B: VldE


Theoretical massNumber of molelcules
Total (without water)110,0132
Polymers110,0132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area4040 Å2
ΔGint4 kcal/mol
Surface area38470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.237, 48.562, 123.049
Angle α, β, γ (deg.)90.00, 91.88, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: Protein VldE / pseudo-glycosyltransferase


Mass: 55006.535 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces hygroscopicus subsp. limoneus (bacteria)
Gene: vldE / Production host: Escherichia coli (E. coli)
References: UniProt: Q15JG1, Transferases; Glycosyltransferases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 489 / 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: 2.31 Å3/Da / Density % sol: 46.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100 mM Tris-HCl, pH 8.0, 20-35% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9479 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 18, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9479 Å / Relative weight: 1
ReflectionResolution: 1.98→122.983 Å / Num. all: 70660 / Num. obs: 69317 / % possible obs: 98.1 % / Observed criterion σ(F): 2.7 / Observed criterion σ(I): 2.7
Reflection shellResolution: 1.98→2.08 Å / % possible all: 91.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
REFMAC5.5.0110refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→49.103 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.946 / SU B: 9.22 / SU ML: 0.117 / Cross valid method: THROUGHOUT / σ(F): 2.7 / ESU R: 0.182 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22191 3559 5.1 %RANDOM
Rwork0.18754 ---
obs0.18933 66548 98.75 %-
all-67391 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.854 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å20 Å2-0.44 Å2
2--0.31 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.98→49.103 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7474 0 0 489 7963
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0217648
X-RAY DIFFRACTIONr_angle_refined_deg1.6731.93810427
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4755955
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.67322.732388
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.149151166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2961592
X-RAY DIFFRACTIONr_chiral_restr0.1260.21140
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0216040
X-RAY DIFFRACTIONr_mcbond_it1.3721.54774
X-RAY DIFFRACTIONr_mcangle_it2.12427647
X-RAY DIFFRACTIONr_scbond_it3.4732874
X-RAY DIFFRACTIONr_scangle_it5.154.52780
LS refinement shellResolution: 1.98→2.03 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 265 -
Rwork0.293 4608 -
obs--92.57 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.2986-1.72230.24481.5458-0.26680.2672-0.2093-0.37470.20440.14620.16720.0110.0331-0.26070.0420.1657-0.0115-0.00930.4302-0.1770.19089.623-16.48121.964
21.60240.2968-0.17060.29350.07110.7262-0.0538-0.24860.1340.0364-0.02260.0280.0996-0.07730.07640.18810.0109-0.06020.0807-0.03620.138631.968-21.49113.974
30.7863-0.20620.1520.79-0.39241.1922-0.05460.15860.14220.097-0.03370.0106-0.0954-0.26590.08830.15070.023-0.08070.1432-0.01040.168620.492-10.244-8.017
41.6456-0.60220.70740.436-0.84121.9846-0.2521-0.3183-0.07520.0633-0.0392-0.1145-0.08830.38160.29130.1480.0285-0.01290.32630.06930.209733.817-34.708-39.068
51.78890.0330.44130.2755-0.07960.793-0.2187-0.25120.00940.0290.0786-0.0551-0.16520.01070.14010.22060.0397-0.02010.07730.00110.099112.381-28.689-47.73
61.0595-0.2131-0.01450.83990.2851.1137-0.15240.2369-0.1340.05440.0565-0.10380.00490.3040.09590.1239-0.03320.0360.1436-0.00740.139124.269-40.31-69.2
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 87
2X-RAY DIFFRACTION2A88 - 268
3X-RAY DIFFRACTION3A269 - 481
4X-RAY DIFFRACTION4B4 - 92
5X-RAY DIFFRACTION5B93 - 268
6X-RAY DIFFRACTION6B269 - 481

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