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- PDB-4f9f: Crystal Structure of VldE, the pseudo-glycosyltransferase, in com... -

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Basic information

Entry
Database: PDB / ID: 4f9f
TitleCrystal Structure of VldE, the pseudo-glycosyltransferase, in complex with GDP and Trehalose
ComponentsVldE
KeywordsTRANSFERASE / Twin Rossmann Fold
Function / homology
Function and homology information


validamine 7-phosphate valienyltransferase / trehalose biosynthetic process / hexosyltransferase activity / 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
trehalose / GUANOSINE-5'-DIPHOSPHATE / Validamine 7-phosphate valienyltransferase
Similarity search - Component
Biological speciesStreptomyces hygroscopicus subsp. limoneus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.807 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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
C: VldE
D: VldE
E: VldE
F: VldE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)333,38314
Polymers330,0396
Non-polymers3,3448
Water3,639202
1
A: VldE
B: VldE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,2425
Polymers110,0132
Non-polymers1,2293
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6310 Å2
ΔGint-21 kcal/mol
Surface area35830 Å2
MethodPISA
2
C: VldE
F: VldE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,8994
Polymers110,0132
Non-polymers8862
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5820 Å2
ΔGint-8 kcal/mol
Surface area34780 Å2
MethodPISA
3
D: VldE
E: VldE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,2425
Polymers110,0132
Non-polymers1,2293
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6360 Å2
ΔGint-17 kcal/mol
Surface area35650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)320.821, 122.823, 93.857
Angle α, β, γ (deg.)90.00, 91.62, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'A'
211chain 'D'
112chain 'B'
212chain 'E'
113chain 'C'
213chain 'F'

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
VldE / pseudo-glycosyltransferase


Mass: 55006.535 Da / Num. of mol.: 6
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: Polysaccharide alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose / trehalose /


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: trehalose
DescriptorTypeProgram
DGlcpa1-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a1-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.8 Å3/Da / Density % sol: 56.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 50 mM Tris-HCl, pH 8.0, 18-28% PEG3350, 200-500 mM sodium chloride, 20 mM magnesium chloride, 3% trehalose, 1 mM GDP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 3, 2012
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.807→49.153 Å / Num. all: 88665 / Num. obs: 88243 / % possible obs: 99.3 % / Observed criterion σ(F): 2.5 / Observed criterion σ(I): 2.5
Reflection shellResolution: 2.807→2.96 Å / % possible all: 98.5

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIXmodel building
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.807→49.153 Å / SU ML: 0.43 / σ(F): 1.34 / Phase error: 28.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2582 4421 5.02 %RANDOM
Rwork0.2112 ---
obs0.2136 88139 99.05 %-
all-88665 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.29 Å2 / ksol: 0.316 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.5543 Å20 Å214.595 Å2
2---0.8098 Å20 Å2
3---9.3641 Å2
Refinement stepCycle: LAST / Resolution: 2.807→49.153 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21796 0 214 202 22212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01622520
X-RAY DIFFRACTIONf_angle_d1.46630713
X-RAY DIFFRACTIONf_dihedral_angle_d16.3268141
X-RAY DIFFRACTIONf_chiral_restr0.1773371
X-RAY DIFFRACTIONf_plane_restr0.0074042
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3678X-RAY DIFFRACTIONPOSITIONAL
12D3678X-RAY DIFFRACTIONPOSITIONAL0.534
21B3610X-RAY DIFFRACTIONPOSITIONAL
22E3610X-RAY DIFFRACTIONPOSITIONAL0.691
31C3605X-RAY DIFFRACTIONPOSITIONAL
32F3605X-RAY DIFFRACTIONPOSITIONAL0.481
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.807-2.83910.33671380.31942629X-RAY DIFFRACTION94
2.8391-2.87250.3381450.30772754X-RAY DIFFRACTION100
2.8725-2.90760.34131300.30212844X-RAY DIFFRACTION100
2.9076-2.94440.4411380.29752790X-RAY DIFFRACTION100
2.9444-2.98310.37931400.29762797X-RAY DIFFRACTION100
2.9831-3.0240.34781570.28692832X-RAY DIFFRACTION100
3.024-3.06720.32431340.28192775X-RAY DIFFRACTION100
3.0672-3.11290.3661530.2742774X-RAY DIFFRACTION100
3.1129-3.16160.32081440.26442811X-RAY DIFFRACTION100
3.1616-3.21340.32261320.2612829X-RAY DIFFRACTION100
3.2134-3.26880.31291500.2482745X-RAY DIFFRACTION100
3.2688-3.32820.28821360.24182837X-RAY DIFFRACTION100
3.3282-3.39220.28371580.24572799X-RAY DIFFRACTION100
3.3922-3.46140.31951340.27862710X-RAY DIFFRACTION96
3.4614-3.53670.33761380.23952813X-RAY DIFFRACTION100
3.5367-3.61890.2661610.23162795X-RAY DIFFRACTION99
3.6189-3.70940.31781410.26532687X-RAY DIFFRACTION96
3.7094-3.80970.27961530.20642811X-RAY DIFFRACTION100
3.8097-3.92170.29441250.23222700X-RAY DIFFRACTION95
3.9217-4.04820.26531360.1842807X-RAY DIFFRACTION99
4.0482-4.19290.2111570.16362794X-RAY DIFFRACTION100
4.1929-4.36060.21971350.15472803X-RAY DIFFRACTION100
4.3606-4.5590.18681770.14842815X-RAY DIFFRACTION100
4.559-4.79910.18511350.1532815X-RAY DIFFRACTION100
4.7991-5.09950.21311780.16482815X-RAY DIFFRACTION100
5.0995-5.49280.21211640.18062799X-RAY DIFFRACTION100
5.4928-6.04470.27231780.21512784X-RAY DIFFRACTION100
6.0447-6.91730.25231270.21572870X-RAY DIFFRACTION100
6.9173-8.70710.19121680.16822830X-RAY DIFFRACTION100
8.7071-49.16040.19941590.17442854X-RAY DIFFRACTION98

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