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- PDB-3vdn: Crystal Structure of VldE, the pseudo-glycosyltransferase, in com... -

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Basic information

Entry
Database: PDB / ID: 3vdn
TitleCrystal Structure of VldE, the pseudo-glycosyltransferase, in complex with GDP
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
GUANOSINE-5'-DIPHOSPHATE / Validamine 7-phosphate valienyltransferase
Similarity search - Component
Biological speciesStreptomyces hygroscopicus subsp. limoneus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsCavalier, M.C. / Yim, Y.-S. / Asamizu, S. / Neau, D. / Mahmud, T. / Lee, Y.-H.
CitationJournal: To be Published
Title: Crystal Structure of the 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: VldE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4502
Polymers55,0071
Non-polymers4431
Water1,15364
1
B: VldE
hetero molecules

B: VldE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,8994
Polymers110,0132
Non-polymers8862
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area5420 Å2
ΔGint-5 kcal/mol
Surface area37420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.029, 121.037, 47.824
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein VldE / pseudo-glycosyltransferase


Mass: 55006.535 Da / Num. of mol.: 1
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: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.21 Å3/Da / Density % sol: 44.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100 mM Tris-HCl, pH 8.0, 20-35% PEG3350, 3 mM GDP, 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: 0.9792 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: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.55→44.48 Å / Num. all: 16553 / Num. obs: 16222 / % possible obs: 98 % / Observed criterion σ(F): 2.8 / Observed criterion σ(I): 2.8
Reflection shellResolution: 2.55→2.69 Å / % possible all: 86.8

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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: 2.55→44.48 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.86 / SU B: 31.639 / SU ML: 0.325 / Cross valid method: THROUGHOUT / σ(F): 2.8 / ESU R: 2.714 / ESU R Free: 0.368 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28573 814 5 %RANDOM
Rwork0.24064 ---
obs0.24296 15385 100 %-
all-15385 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.266 Å2
Baniso -1Baniso -2Baniso -3
1-1.94 Å20 Å20 Å2
2---0.49 Å20 Å2
3----1.46 Å2
Refinement stepCycle: LAST / Resolution: 2.55→44.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3704 0 28 64 3796
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0213820
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5561.9465214
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5235472
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.88922.76192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.7215577
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0921545
X-RAY DIFFRACTIONr_chiral_restr0.1050.2570
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213001
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_it0.6461.52365
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.16723789
X-RAY DIFFRACTIONr_scbond_it1.88131455
X-RAY DIFFRACTIONr_scangle_it3.0014.51425
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.55→2.617 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 40 -
Rwork0.318 839 -
obs--100 %
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)
13.2806-0.2839-1.74641.7610.2995-0.0193-0.06470.5144-0.21680.0090.0822-0.38180.0352-0.0686-0.01750.2313-0.03710.0750.5571-0.10420.3525-12.066-21.95314.066
21.8099-0.24270.31670.524-0.21170.3369-0.08870.0519-0.10920.03830.0404-0.01240.2024-0.02270.04830.2806-0.040.0270.2738-0.00840.198-32.24-13.70821.537
30.93560.2189-0.14430.8692-0.88261.2558-0.05540.12250.13540.0221-0.0578-0.16690.10490.03980.11320.2106-0.04720.01130.2875-0.01280.2251-19.9757.5799.199
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B4 - 98
2X-RAY DIFFRACTION2B99 - 268
3X-RAY DIFFRACTION3B269 - 481

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