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- PDB-8iye: Structure of VldE-D158N in complex with GDP -

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Basic information

Entry
Database: PDB / ID: 8iye
TitleStructure of VldE-D158N 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-D158N 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

Downloads & links

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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)110,8974
Polymers110,0112
Non-polymers8862
Water8,953497
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-4 kcal/mol
Surface area36690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.044, 84.567, 120.928
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
Noncrystallographic symmetry (NCS)NCS oper: (Code: givenMatrix: (0.999999898868, 0.000338918247345, -0.000295631975658), (0.000339077038492, -0.9999997982, 0.000537239752688), (-0.000295449835644, -0.00053733994037, -0.999999811988) ...NCS oper: (Code: given
Matrix: (0.999999898868, 0.000338918247345, -0.000295631975658), (0.000339077038492, -0.9999997982, 0.000537239752688), (-0.000295449835644, -0.00053733994037, -0.999999811988)
Vector: -0.0120523647625, -0.655231988173, -60.4597407117)

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Components

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


Mass: 55005.547 Da / Num. of mol.: 2 / Mutation: D158N
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: isolated from a natural source / 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.: 497 / 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: 2.23 Å3/Da / Density % sol: 44.92 %
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→48.04 Å / Num. obs: 74663 / % possible obs: 97.9 % / Redundancy: 4.1 % / Biso Wilson estimate: 27.34 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.094 / Net I/σ(I): 6.7
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 0.544 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4474 / CC1/2: 0.85

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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→48.04 Å / SU ML: 0.2799 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 32.3116
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2831 3682 4.94 %
Rwork0.2357 70917 -
obs0.238 74599 97.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.37 Å2
Refinement stepCycle: LAST / Resolution: 1.9→48.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7352 0 56 497 7905
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00327584
X-RAY DIFFRACTIONf_angle_d0.685110356
X-RAY DIFFRACTIONf_chiral_restr0.04431136
X-RAY DIFFRACTIONf_plane_restr0.00651370
X-RAY DIFFRACTIONf_dihedral_angle_d16.04852722
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.930.36171470.2942742X-RAY DIFFRACTION96.24
1.93-1.950.33451670.28082680X-RAY DIFFRACTION99.62
1.95-1.980.32781190.27662785X-RAY DIFFRACTION98.27
1.98-2.010.3011300.27472686X-RAY DIFFRACTION96.17
2.01-2.040.30351520.27662731X-RAY DIFFRACTION99.48
2.04-2.070.31531550.26522688X-RAY DIFFRACTION97.5
2.07-2.110.33821600.27592655X-RAY DIFFRACTION97.61
2.11-2.150.34211520.27542753X-RAY DIFFRACTION98.98
2.15-2.190.33391460.27452687X-RAY DIFFRACTION96.03
2.19-2.230.38241370.27322710X-RAY DIFFRACTION98.79
2.23-2.280.31281590.28212754X-RAY DIFFRACTION96.81
2.28-2.340.36261220.28422649X-RAY DIFFRACTION97.71
2.34-2.390.31651080.27422775X-RAY DIFFRACTION97.14
2.39-2.460.30061440.2792683X-RAY DIFFRACTION97.18
2.46-2.530.33271530.27472700X-RAY DIFFRACTION96.39
2.53-2.610.36321470.27762677X-RAY DIFFRACTION97.85
2.61-2.710.38191290.27772722X-RAY DIFFRACTION96.78
2.71-2.810.31681350.27792740X-RAY DIFFRACTION97.23
2.81-2.940.351330.27762708X-RAY DIFFRACTION97.23
2.94-3.10.27771290.27362736X-RAY DIFFRACTION97.28
3.1-3.290.29551690.25212678X-RAY DIFFRACTION97.87
3.29-3.550.28541390.22142762X-RAY DIFFRACTION98.31
3.55-3.90.22711380.2032785X-RAY DIFFRACTION98.65
3.9-4.470.19011310.18322786X-RAY DIFFRACTION98.91
4.47-5.630.21031320.17882797X-RAY DIFFRACTION99.02
5.63-48.040.23891490.17342848X-RAY DIFFRACTION98.65
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)
12.2797786048-2.61244370810.01956561802063.36124781499-0.3559827710410.467598394862-0.223015188917-0.06176025280080.32143642014-0.2989726381420.01575850212320.10201864402-0.443627649624-0.1689353620030.2013447084570.5243460888180.0237555465084-0.08793964408530.351731451685-0.05268303685890.329148936131-8.6020800448832.0914607639-51.9131584822
20.7209278887860.903202025492-0.2070822921662.66919439214-0.4759103270281.91967380574-0.0233994282570.0887754849650.0380395218744-0.242270513382-0.05261796163390.0574723085703-0.04962703618320.08519498872220.07093169827710.1459965481560.0299056657107-0.01681690556830.331318668207-0.079274006560.179420237716-3.478239287289.30140632601-44.4239850595
31.065263464810.202261253198-0.3189518582981.029326491540.2015303204011.517322410590.082563080030.140758125050.03092833126580.0618092560447-0.1442785713330.196892604237-0.257962703951-0.2538036406420.05960875279520.1933655040670.0138084520436-0.009543469851270.485414115722-0.08129484313070.245049453499-14.978882394121.7008870224-22.6682181577
43.721074601284.75814249507-0.2801017765626.03074958689-0.3634276756440.101904673573-0.4723981385980.315155079259-0.400891432874-0.2240988247090.1849572925890.02321366798480.307201977917-0.3773834438170.2711848406550.48513782306-0.09460869607120.1396823605940.540986425283-0.0810407510020.3727875457-11.535478721-35.3945233946-10.6019767124
50.656136009977-0.5092043372820.3367307067912.26163781061-1.081985190451.93731592871-0.0018921590783-0.0474352775897-0.1494688874160.244313063364-0.04149167123070.2774835465650.257420449739-0.01988564072470.01985414843750.27292917077-0.02914707124360.05791406355830.472520860175-0.07307492036370.241690272379-7.65474398453-18.6668225432-9.806145762
60.5338811498130.03945539646640.2448395711241.126456907450.4558568044741.233187149520.0542768528582-0.0793504959858-0.0265460626044-0.0244356123962-0.1325019706940.1223463453090.172463362852-0.1420430453620.06247401306180.1675728058570.00268397428750.02303087253840.475360386906-0.05147045612650.208652319562-10.208513061-18.2598634757-32.953680558
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 88 )AA3 - 881 - 86
22chain 'A' and (resid 89 through 264 )AA89 - 26487 - 262
33chain 'A' and (resid 269 through 481 )AA269 - 481263 - 475
44chain 'B' and (resid 3 through 34 )BC3 - 341 - 32
55chain 'B' and (resid 35 through 180 )BC35 - 18033 - 178
66chain 'B' and (resid 181 through 481 )BC181 - 481179 - 475

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