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- PDB-4f97: Crystal Structure of VldE, the pseudo-glycosyltransferase, in com... -

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Basic information

Entry
Database: PDB / ID: 4f97
TitleCrystal Structure of VldE, the pseudo-glycosyltransferase, in complex with GDP and validoxylamine A 7'-phosphate
ComponentsVldE
KeywordsTRANSFERASE / Twin Rossman Fold
Function / homology
Function and homology information


validamine 7-phosphate valienyltransferase / alpha,alpha-trehalose-phosphate synthase complex (UDP-forming) / trehalose-phosphatase activity / trehalose biosynthetic process / hexosyltransferase activity / trehalose metabolism in response to stress / antibiotic biosynthetic process / cellular response to heat / cytosol
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 / Chem-VDO / Validamine 7-phosphate valienyltransferase
Similarity search - Component
Biological speciesStreptomyces hygroscopicus subsp. limoneus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.108 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

Downloads & links

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Assembly

Deposited unit
A: VldE
B: VldE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,92510
Polymers110,0132
Non-polymers1,9128
Water8,791488
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6310 Å2
ΔGint-24 kcal/mol
Surface area36050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.959, 120.714, 84.236
Angle α, β, γ (deg.)90.00, 91.63, 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 'A' and (resseq 3:263 or resseq 270:479 ) and (not element H) and (not element D)
211chain 'B' and (resseq 3:263 or resseq 270:479 ) and (not element H) and (not element D)

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 496 molecules

#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-VDO / [(1R,2R,3S,4S,5S)-2,3,4-TRIHYDROXY-5-{[(1S,4R,5S,6S)-4,5,6-TRIHYDROXY-3-(HYDROXYMETHYL)CYCLOHEX-2-EN-1-YL]AMINO}CYCLOHEXYL]METHYL DIHYDROGEN PHOSPHATE


Mass: 415.330 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H26NO11P
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 488 / 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: 44.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100 mM Tris-HCl, pH 8.0, 25-30% PEG3350, 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: 2.108→47.94 Å / Num. all: 55145 / Num. obs: 55049 / % possible obs: 99.7 % / Observed criterion σ(F): 2.7 / Observed criterion σ(I): 2.7
Reflection shellResolution: 2.108→2.22 Å / % possible all: 99

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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: 2.108→47.94 Å / SU ML: 0.28 / σ(F): 1.35 / Phase error: 22.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2222 2790 5.07 %RANDOM
Rwork0.1906 ---
obs0.1922 55049 99.66 %-
all-55145 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.611 Å2 / ksol: 0.328 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.6679 Å20 Å22.6121 Å2
2---3.4823 Å20 Å2
3---1.8144 Å2
Refinement stepCycle: LAST / Resolution: 2.108→47.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7361 0 120 488 7969
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0177652
X-RAY DIFFRACTIONf_angle_d1.76310443
X-RAY DIFFRACTIONf_dihedral_angle_d15.5562764
X-RAY DIFFRACTIONf_chiral_restr0.1621150
X-RAY DIFFRACTIONf_plane_restr0.0071372
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3661X-RAY DIFFRACTIONPOSITIONAL
12B3661X-RAY DIFFRACTIONPOSITIONAL0.401
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.108-2.14450.30121280.26292520X-RAY DIFFRACTION97
2.1445-2.18350.27611430.24342656X-RAY DIFFRACTION100
2.1835-2.22550.29711380.23782590X-RAY DIFFRACTION100
2.2255-2.2710.31131530.24362609X-RAY DIFFRACTION100
2.271-2.32030.28551270.2332597X-RAY DIFFRACTION100
2.3203-2.37430.26621530.2312610X-RAY DIFFRACTION100
2.3743-2.43370.24231270.22572596X-RAY DIFFRACTION100
2.4337-2.49950.26311480.20882607X-RAY DIFFRACTION100
2.4995-2.5730.24881360.20112625X-RAY DIFFRACTION100
2.573-2.65610.21091330.20012638X-RAY DIFFRACTION100
2.6561-2.7510.25771260.19622603X-RAY DIFFRACTION100
2.751-2.86110.27261330.19972620X-RAY DIFFRACTION100
2.8611-2.99130.23861570.19852615X-RAY DIFFRACTION100
2.9913-3.1490.23271170.20542631X-RAY DIFFRACTION100
3.149-3.34620.22991370.19552620X-RAY DIFFRACTION100
3.3462-3.60450.21551420.18182609X-RAY DIFFRACTION100
3.6045-3.96710.19231300.16532624X-RAY DIFFRACTION99
3.9671-4.54080.17591420.15142610X-RAY DIFFRACTION100
4.5408-5.71940.18291590.16772613X-RAY DIFFRACTION99
5.7194-47.95190.19841610.18442626X-RAY DIFFRACTION99

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