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- PDB-8iyf: Structure of VldE-H182A in complex with GDP -

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Basic information

Entry
Database: PDB / ID: 8iyf
TitleStructure of VldE-H182A in complex with GDP
ComponentsValidamine 7-phosphate valienyltransferase
KeywordsTRANSFERASE / Pseudoglycosyltransferase / validamine
Function / homologyvalidamine 7-phosphate valienyltransferase / alpha,alpha-trehalose-phosphate synthase (UDP-forming) activity / Glycosyl transferase, family 20 / Glycosyltransferase family 20 / trehalose biosynthetic process / antibiotic biosynthetic process / GUANOSINE-5'-DIPHOSPHATE / Validamine 7-phosphate valienyltransferase
Function and homology information
Biological speciesStreptomyces hygroscopicus subsp. limoneus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWong, C.P. / Mori, T. / Mahmud, T. / Abe, I.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of VldE-H182A in complex with GDP
Authors: Wong, C.P. / Mori, T. / Mahmud, T. / Abe, I.
History
DepositionApr 4, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Validamine 7-phosphate valienyltransferase
B: Validamine 7-phosphate valienyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,7654
Polymers109,8792
Non-polymers8862
Water10,593588
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-5 kcal/mol
Surface area36730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.009, 121.263, 84.544
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Validamine 7-phosphate valienyltransferase / Pseudoglycosyltransferase / Trehalose 6-phosphate synthase-like enzyme VldE


Mass: 54939.465 Da / Num. of mol.: 2 / Mutation: H182A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces hygroscopicus subsp. limoneus (bacteria)
Gene: vldE, SHL15_8006 / Production host: Escherichia coli (E. coli)
References: UniProt: Q15JG1, validamine 7-phosphate valienyltransferase
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 588 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.24 Å3/Da / Density % sol: 45.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM Tris-HCl, pH8.5, 26% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→48.01 Å / Num. obs: 74391 / % possible obs: 97.9 % / Redundancy: 4.4 % / Biso Wilson estimate: 26.21 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.3
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 0.518 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4500 / CC1/2: 0.805

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→48.01 Å / SU ML: 0.2376 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 25.4978
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2411 2002 2.69 %
Rwork0.1953 72348 -
obs0.1965 74350 97.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.83 Å2
Refinement stepCycle: LAST / Resolution: 1.9→48.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7356 0 56 589 8001
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00737586
X-RAY DIFFRACTIONf_angle_d0.97210358
X-RAY DIFFRACTIONf_chiral_restr0.05611139
X-RAY DIFFRACTIONf_plane_restr0.00921369
X-RAY DIFFRACTIONf_dihedral_angle_d15.26612728
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.32691450.26735246X-RAY DIFFRACTION98.61
1.95-20.31841480.23765217X-RAY DIFFRACTION98.6
2-2.060.25871420.22275170X-RAY DIFFRACTION99.25
2.06-2.130.24151420.21455209X-RAY DIFFRACTION98.73
2.13-2.20.24351490.20395229X-RAY DIFFRACTION98.82
2.2-2.290.27481450.21465235X-RAY DIFFRACTION98.75
2.29-2.390.25561430.20565130X-RAY DIFFRACTION98.25
2.39-2.520.27381420.20775160X-RAY DIFFRACTION97.64
2.52-2.680.24491410.21085154X-RAY DIFFRACTION97.48
2.68-2.880.25931400.21375109X-RAY DIFFRACTION96.9
2.88-3.170.22881360.20795079X-RAY DIFFRACTION96.01
3.17-3.630.25771410.18365053X-RAY DIFFRACTION95.3
3.63-4.580.19921370.16525106X-RAY DIFFRACTION96.34
4.58-48.010.21741510.1755251X-RAY DIFFRACTION97.72

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