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- PDB-8rdh: Crystal structure of UDP-galactose 4-epimerase from Pyrococcus ho... -

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Basic information

Entry
Database: PDB / ID: 8rdh
TitleCrystal structure of UDP-galactose 4-epimerase from Pyrococcus horikoshii with bound NAD and GDP-L-fucose
ComponentsSDR family NAD(P)-dependent oxidoreductase
KeywordsISOMERASE / UDP-galactose 4-epimerase / GALE / Rossmann fold / GDP-L-fucose
Function / homologyNAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding domain superfamily / GUANOSINE-5'-DIPHOSPHATE-BETA-L-FUCOPYRANOSE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / SDR family NAD(P)-dependent oxidoreductase
Function and homology information
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsThunnissen, A.M.W.H. / Alvarez Quispe, C. / Desmet, T.
Funding support Belgium, 2items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)1105922N Belgium
Research Foundation - Flanders (FWO)G0A7520N Belgium
CitationJournal: To Be Published
Title: Structural, computational and biochemical analysis reveal new insights in the specificity of a promiscuous GDP-Gal4E
Authors: Alvarez Quispe, C. / Savino, S. / Biarnes, X. / Planas, A. / Thunnissen, A.M.W.H. / Beerens, K. / Desmet, T.
History
DepositionDec 8, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 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: SDR family NAD(P)-dependent oxidoreductase
B: SDR family NAD(P)-dependent oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,9296
Polymers73,4242
Non-polymers2,5064
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5550 Å2
ΔGint-35 kcal/mol
Surface area22760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.331, 97.262, 117.252
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SDR family NAD(P)-dependent oxidoreductase


Mass: 36711.793 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: HA331_04725 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A832T930
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-GFB / GUANOSINE-5'-DIPHOSPHATE-BETA-L-FUCOPYRANOSE


Mass: 589.342 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H25N5O15P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 44.75 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein was concentrated in 20 mM MOPS, pH 7, 0.2 mM TCEP to 8-10 mg/ml. Crystallization solution contained 0.2 M KSCN, 0.1 M Bis-Tris propane, pH 7.5, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965459 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965459 Å / Relative weight: 1
ReflectionResolution: 2.4→48.63 Å / Num. obs: 25732 / % possible obs: 97.8 % / Redundancy: 3.9 % / CC1/2: 0.987 / Rmerge(I) obs: 0.193 / Rpim(I) all: 0.104 / Rrim(I) all: 0.22 / Χ2: 1.04 / Net I/σ(I): 7.9 / Num. measured all: 101080
Reflection shellResolution: 2.4→2.49 Å / % possible obs: 88.5 % / Redundancy: 2.8 % / Rmerge(I) obs: 1.113 / Num. measured all: 6739 / Num. unique obs: 2395 / CC1/2: 0.478 / Rpim(I) all: 0.743 / Rrim(I) all: 1.346 / Χ2: 0.9 / Net I/σ(I) obs: 1.1

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→48.63 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2454 1297 5.06 %
Rwork0.1885 --
obs0.1914 25652 97.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→48.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5002 0 164 68 5234
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035274
X-RAY DIFFRACTIONf_angle_d0.7027157
X-RAY DIFFRACTIONf_dihedral_angle_d14.1992102
X-RAY DIFFRACTIONf_chiral_restr0.044808
X-RAY DIFFRACTIONf_plane_restr0.007895
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.50.30961240.28232420X-RAY DIFFRACTION88
2.5-2.610.26471350.24922654X-RAY DIFFRACTION97
2.61-2.750.34661640.25612651X-RAY DIFFRACTION98
2.75-2.920.32481220.2132755X-RAY DIFFRACTION100
2.92-3.140.28431500.20962746X-RAY DIFFRACTION100
3.14-3.460.26181660.18772697X-RAY DIFFRACTION98
3.46-3.960.21551370.16332742X-RAY DIFFRACTION98
3.96-4.990.19581600.13882782X-RAY DIFFRACTION99
4.99-48.630.2061390.17942908X-RAY DIFFRACTION98

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