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- PDB-4f96: Crystal Structure of VldE, the pseudo-glycosyltransferase, in com... -

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Basic information

Entry
Database: PDB / ID: 4f96
TitleCrystal Structure of VldE, the pseudo-glycosyltransferase, in complex with GDP
ComponentsVldE
KeywordsTRANSFERASE / Twin Rossman 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: 2.152 Å
AuthorsCavalier, M.C. / Yim, Y.-S. / Asamizu, S. / Neau, D. / Almabruk, K.H. / Mahmud, T. / Lee, Y.-H.
CitationJournal: Plos One / Year: 2012
Title: Mechanistic Insights into Validoxylamine A 7'-Phosphate Synthesis by VldE Using the Structure of the Entire Product Complex.
Authors: Cavalier, M.C. / Yim, Y.S. / Asamizu, S. / Neau, D. / Almabruk, K.H. / Mahmud, T. / Lee, Y.H.
History
DepositionMay 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: 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
A: VldE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,9706
Polymers110,0132
Non-polymers9574
Water7,296405
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint-32 kcal/mol
Surface area37030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.821, 121.151, 84.333
Angle α, β, γ (deg.)90.00, 91.74, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'B' and (resseq 4:261 or resseq 269:481 ) and (not element H) and (not element D)
211chain 'A' and (resseq 4:261 or resseq 269:481 ) and (not element H) and (not element D)

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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: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / 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: 2.22 Å3/Da / Density % sol: 44.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100 mM Tris-HCl, pH 8.0, 30-35% PEG3350, 3 mM GDP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 2, 2012
RadiationMonochromator: Si(111) channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→37.77 Å / Num. all: 52004 / Num. obs: 51924 / % possible obs: 99.9 % / Observed criterion σ(F): 3.1 / Observed criterion σ(I): 3.1
Reflection shellResolution: 2.15→2.23 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.152→37.524 Å / SU ML: 0.29 / σ(F): 1.35 / Phase error: 20.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2092 2645 5.09 %RANDOM
Rwork0.1898 ---
obs0.1908 51924 99.84 %-
all-50004 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.866 Å2 / ksol: 0.348 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.0034 Å20 Å24.259 Å2
2---4.5416 Å2-0 Å2
3----0.4619 Å2
Refinement stepCycle: LAST / Resolution: 2.152→37.524 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7378 0 58 405 7841
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0127610
X-RAY DIFFRACTIONf_angle_d1.29710384
X-RAY DIFFRACTIONf_dihedral_angle_d14.8332758
X-RAY DIFFRACTIONf_chiral_restr0.0831134
X-RAY DIFFRACTIONf_plane_restr0.0071374
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B3681X-RAY DIFFRACTIONPOSITIONAL
12A3681X-RAY DIFFRACTIONPOSITIONAL0.314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.152-2.19120.24311350.2452545X-RAY DIFFRACTION98
2.1912-2.23330.31871350.23952626X-RAY DIFFRACTION100
2.2333-2.27890.30681410.24292611X-RAY DIFFRACTION100
2.2789-2.32850.23651530.23862541X-RAY DIFFRACTION100
2.3285-2.38260.24561360.21932594X-RAY DIFFRACTION100
2.3826-2.44220.24341370.22522568X-RAY DIFFRACTION100
2.4422-2.50820.24351430.21332603X-RAY DIFFRACTION100
2.5082-2.5820.26171340.21412570X-RAY DIFFRACTION100
2.582-2.66530.21181350.20882624X-RAY DIFFRACTION100
2.6653-2.76050.22061300.19872590X-RAY DIFFRACTION100
2.7605-2.8710.19281450.19822565X-RAY DIFFRACTION100
2.871-3.00160.23651410.20082627X-RAY DIFFRACTION100
3.0016-3.15980.26411290.20772603X-RAY DIFFRACTION100
3.1598-3.35770.20571370.20052606X-RAY DIFFRACTION100
3.3577-3.61670.2031550.18262559X-RAY DIFFRACTION100
3.6167-3.98030.19191260.1722629X-RAY DIFFRACTION100
3.9803-4.55540.17211490.14862572X-RAY DIFFRACTION100
4.5554-5.73610.17221380.16562631X-RAY DIFFRACTION100
5.7361-37.52950.18811460.18322615X-RAY DIFFRACTION99

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