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

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Basic information

Entry
Database: PDB / ID: 8rdg
TitleCrystal structure of UDP-galactose 4-epimerase from Pyrococcus horikoshii with bound NAD
ComponentsSDR family NAD(P)-dependent oxidoreductase
KeywordsISOMERASE / UDP-galactose 4-epimerase / GALE / Rossmann fold / NAD
Function / homologyNAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding domain superfamily / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / SDR family NAD(P)-dependent oxidoreductase
Function and homology information
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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

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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)74,7504
Polymers73,4242
Non-polymers1,3272
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5550 Å2
ΔGint-34 kcal/mol
Surface area23490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.380, 78.089, 128.282
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.09 Å3/Da / Density % sol: 41.25 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein was concentrated to 8-10 mg/ml in 20 mM MOPS, pH 7, 0.2 mM TCEP. Crystallization solution contained 0.1 M Na-propionate/Na-cacodylate/Bis-Tris propane, pH 7, 25% (w/v) PEG1500

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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: 1.9→49.56 Å / Num. obs: 49239 / % possible obs: 99.7 % / Redundancy: 6.5 % / CC1/2: 0.993 / Rmerge(I) obs: 0.214 / Rpim(I) all: 0.09 / Rrim(I) all: 0.233 / Χ2: 1.04 / Net I/σ(I): 7.1 / Num. measured all: 320337
Reflection shellResolution: 1.9→1.94 Å / % possible obs: 98.5 % / Redundancy: 6.5 % / Rmerge(I) obs: 2.105 / Num. measured all: 20229 / Num. unique obs: 3101 / CC1/2: 0.489 / Rpim(I) all: 0.883 / Rrim(I) all: 2.286 / Χ2: 1.09 / Net I/σ(I) obs: 1

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_4958: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→49.56 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0.1 / Phase error: 25.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2302 4638 4.99 %
Rwork0.1928 --
obs0.1947 49159 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→49.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4969 0 88 242 5299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075180
X-RAY DIFFRACTIONf_angle_d0.8637015
X-RAY DIFFRACTIONf_dihedral_angle_d12.2941900
X-RAY DIFFRACTIONf_chiral_restr0.052778
X-RAY DIFFRACTIONf_plane_restr0.007893
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.37651560.33782936X-RAY DIFFRACTION97
1.92-1.940.33161360.31922866X-RAY DIFFRACTION97
1.94-1.970.31951570.30752946X-RAY DIFFRACTION99
1.97-1.990.3621460.29572978X-RAY DIFFRACTION100
1.99-2.020.38051350.29352945X-RAY DIFFRACTION99
2.02-2.050.31231410.28423014X-RAY DIFFRACTION99
2.05-2.080.35171350.28492826X-RAY DIFFRACTION96
2.08-2.110.29331630.26312959X-RAY DIFFRACTION99
2.11-2.140.32641610.25512916X-RAY DIFFRACTION100
2.14-2.170.28351580.23762992X-RAY DIFFRACTION99
2.17-2.210.2841780.23732920X-RAY DIFFRACTION100
2.21-2.250.2741570.23642940X-RAY DIFFRACTION99
2.25-2.30.28141590.22372971X-RAY DIFFRACTION99
2.3-2.340.25181700.21112928X-RAY DIFFRACTION100
2.34-2.390.23581610.20042942X-RAY DIFFRACTION100
2.39-2.450.29051870.21042932X-RAY DIFFRACTION100
2.45-2.510.23661800.2052941X-RAY DIFFRACTION100
2.51-2.580.26221300.2093013X-RAY DIFFRACTION100
2.58-2.650.27431640.18942936X-RAY DIFFRACTION100
2.65-2.740.23251340.19962956X-RAY DIFFRACTION99
2.74-2.840.23551560.20012964X-RAY DIFFRACTION100
2.84-2.950.23541530.19192948X-RAY DIFFRACTION99
2.95-3.090.20831460.19162952X-RAY DIFFRACTION99
3.09-3.250.22831770.17842965X-RAY DIFFRACTION100
3.25-3.450.20731620.16312941X-RAY DIFFRACTION99
3.45-3.720.17561650.1522937X-RAY DIFFRACTION100
3.72-4.090.18871530.14182966X-RAY DIFFRACTION99
4.09-4.680.13011260.12342989X-RAY DIFFRACTION99
4.69-5.90.16361380.14532898X-RAY DIFFRACTION97
5.9-49.560.17451540.15742942X-RAY DIFFRACTION99

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