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

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Basic information

Entry
Database: PDB / ID: 8rdi
TitleCrystal structure of UDP-galactose 4-epimerase from Pyrococcus horikoshii containing Y145F mutation and 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: 3.1 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
C: SDR family NAD(P)-dependent oxidoreductase
D: SDR family NAD(P)-dependent oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,79412
Polymers146,7834
Non-polymers5,0118
Water00
1
A: SDR family NAD(P)-dependent oxidoreductase
B: SDR family NAD(P)-dependent oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8976
Polymers73,3922
Non-polymers2,5064
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-36 kcal/mol
Surface area22880 Å2
MethodPISA
2
C: SDR family NAD(P)-dependent oxidoreductase
D: SDR family NAD(P)-dependent oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8976
Polymers73,3922
Non-polymers2,5064
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-36 kcal/mol
Surface area22800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.671, 169.978, 80.074
Angle α, β, γ (deg.)90.00, 97.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 36695.793 Da / Num. of mol.: 4 / Mutation: Y145F
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.: 4 / 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.: 4 / Source method: obtained synthetically / Formula: C16H25N5O15P2 / Feature type: SUBJECT OF INVESTIGATION
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: 2.84 Å3/Da / Density % sol: 56.65 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.2
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 NaCl, 0.1 M Na/K phosphate, pH 6.2, 50% PEG 200

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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: 3.1→49.66 Å / Num. obs: 29623 / % possible obs: 99.8 % / Redundancy: 3.4 % / CC1/2: 0.981 / Rmerge(I) obs: 0.212 / Rpim(I) all: 0.135 / Rrim(I) all: 0.252 / Χ2: 0.48 / Net I/σ(I): 3.9 / Num. measured all: 99928
Reflection shellResolution: 3.1→3.29 Å / % possible obs: 99.8 % / Redundancy: 3.3 % / Rmerge(I) obs: 1.117 / Num. measured all: 15822 / Num. unique obs: 4765 / CC1/2: 0.506 / Rpim(I) all: 0.706 / Rrim(I) all: 1.325 / Χ2: 0.45 / Net I/σ(I) obs: 0.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→49.66 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.29 1484 5.02 %
Rwork0.2199 --
obs0.2233 29578 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→49.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9968 0 328 0 10296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410512
X-RAY DIFFRACTIONf_angle_d0.7514260
X-RAY DIFFRACTIONf_dihedral_angle_d13.7084188
X-RAY DIFFRACTIONf_chiral_restr0.0451608
X-RAY DIFFRACTIONf_plane_restr0.0071784
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.20.33661530.27622523X-RAY DIFFRACTION100
3.2-3.310.3581290.27592517X-RAY DIFFRACTION100
3.31-3.450.33291280.26232576X-RAY DIFFRACTION100
3.45-3.60.34461190.25592585X-RAY DIFFRACTION100
3.6-3.790.27771410.232538X-RAY DIFFRACTION100
3.79-4.030.31551380.21282542X-RAY DIFFRACTION100
4.03-4.340.23961140.19882573X-RAY DIFFRACTION100
4.34-4.780.25381460.18072553X-RAY DIFFRACTION99
4.78-5.470.27991400.1942543X-RAY DIFFRACTION100
5.47-6.890.30461340.22652577X-RAY DIFFRACTION100
6.89-49.660.26491420.21262567X-RAY DIFFRACTION99

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