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- PDB-9rl0: CDP-tyvelose 2-epimerase from Thermodesulfatator atlanticus -

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Basic information

Entry
Database: PDB / ID: 9rl0
TitleCDP-tyvelose 2-epimerase from Thermodesulfatator atlanticus
ComponentsCDP-tyvelose 2-epimerase
KeywordsSUGAR BINDING PROTEIN / CDP-tyvelose 2-epimerase
Function / homologyCYTIDINE-5'-DIPHOSPHATE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Function and homology information
Biological speciesThermodesulfatator atlanticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsRapp, C. / van Overtveldt, S. / Pfeiffer, M. / Beerens, K. / Merkas, M. / Pavkov-Keller, T. / Desmet, T. / Nidetzky, B.
Funding support Austria, Belgium, 2items
OrganizationGrant numberCountry
Austrian Science Fund Austria
Research Foundation - Flanders (FWO) Belgium
CitationJournal: J.Biol.Chem. / Year: 2026
Title: A dual catalytic architecture promotes C-2 stereoinversion of CDP-glucose by the CDP-tyvelose 2-epimerase from Thermodesulfatator atlanticus.
Authors: Rapp, C. / van Overtveldt, S. / Sanchez-Murcia, P.A. / Pfeiffer, M. / Beerens, K. / Merkas, M. / Pavkov-Keller, T. / Desmet, T. / Nidetzky, B.
History
DepositionJun 16, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: CDP-tyvelose 2-epimerase
F: CDP-tyvelose 2-epimerase
G: CDP-tyvelose 2-epimerase
H: CDP-tyvelose 2-epimerase
A: CDP-tyvelose 2-epimerase
B: CDP-tyvelose 2-epimerase
C: CDP-tyvelose 2-epimerase
D: CDP-tyvelose 2-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)321,42818
Polymers315,3158
Non-polymers6,11410
Water1448
1
E: CDP-tyvelose 2-epimerase
F: CDP-tyvelose 2-epimerase
G: CDP-tyvelose 2-epimerase
H: CDP-tyvelose 2-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,7149
Polymers157,6574
Non-polymers3,0575
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: CDP-tyvelose 2-epimerase
B: CDP-tyvelose 2-epimerase
C: CDP-tyvelose 2-epimerase
D: CDP-tyvelose 2-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,7149
Polymers157,6574
Non-polymers3,0575
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.415, 90.510, 133.624
Angle α, β, γ (deg.)90.000, 101.193, 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
CDP-tyvelose 2-epimerase


Mass: 39414.316 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermodesulfatator atlanticus (bacteria)
Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-CDP / CYTIDINE-5'-DIPHOSPHATE


Mass: 403.176 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N3O11P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.49 Å3/Da / Density % sol: 50.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: using 0.2 M potassium thiocyanate and 20% PEG 3350 (ShotGun D4) 1 mM NAD+, 1 mM CDP and 7.5 -30 mg/ml protein.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.0723 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 2.6→46.64 Å / Num. obs: 93417 / % possible obs: 97.6 % / Redundancy: 1.7 % / Biso Wilson estimate: 44.04 Å2 / CC1/2: 0.98 / CC star: 0.99 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.124 / Rrim(I) all: 0.179 / Net I/σ(I): 4.06
Reflection shellResolution: 2.6→2.63 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.804 / Num. unique obs: 3388 / CC1/2: 0.43 / CC star: 0.78 / Rpim(I) all: 0.773 / % possible all: 68.7

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
PHASERphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→46.64 Å / SU ML: 0.4035 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.5315
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2893 4666 5 %
Rwork0.2413 88658 -
obs0.2438 93324 97.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.73 Å2
Refinement stepCycle: LAST / Resolution: 2.6→46.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21952 0 402 8 22362
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002822894
X-RAY DIFFRACTIONf_angle_d0.57530880
X-RAY DIFFRACTIONf_chiral_restr0.04383261
X-RAY DIFFRACTIONf_plane_restr0.00463896
X-RAY DIFFRACTIONf_dihedral_angle_d18.62518788
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.630.36791090.32082065X-RAY DIFFRACTION68.67
2.63-2.660.331570.31312981X-RAY DIFFRACTION98.19
2.66-2.690.37921530.31892907X-RAY DIFFRACTION98.27
2.69-2.730.39631570.32312990X-RAY DIFFRACTION98.47
2.73-2.760.36851540.30622918X-RAY DIFFRACTION97.71
2.76-2.80.38161550.30772951X-RAY DIFFRACTION98.6
2.8-2.840.35051560.30172956X-RAY DIFFRACTION97.55
2.84-2.880.37171560.29932967X-RAY DIFFRACTION98.36
2.88-2.930.37521570.29132966X-RAY DIFFRACTION98.83
2.93-2.980.34221540.30092947X-RAY DIFFRACTION98.63
2.98-3.030.33081600.2993029X-RAY DIFFRACTION98.73
3.03-3.080.38771550.29662949X-RAY DIFFRACTION98.48
3.08-3.140.40061560.30132965X-RAY DIFFRACTION98.58
3.14-3.210.371570.29812986X-RAY DIFFRACTION98.62
3.21-3.280.34721550.27842925X-RAY DIFFRACTION98.4
3.28-3.350.32941580.26713016X-RAY DIFFRACTION98.27
3.35-3.440.30181560.25392960X-RAY DIFFRACTION98.73
3.44-3.530.28671570.24072967X-RAY DIFFRACTION98.89
3.53-3.630.29671580.24063006X-RAY DIFFRACTION98.54
3.63-3.750.27741570.24462985X-RAY DIFFRACTION98.43
3.75-3.880.29391560.23592964X-RAY DIFFRACTION98.98
3.88-4.040.25471580.2153017X-RAY DIFFRACTION98.97
4.04-4.220.29211570.21262990X-RAY DIFFRACTION99.12
4.22-4.440.24541590.2023023X-RAY DIFFRACTION99.13
4.45-4.720.19651590.18213005X-RAY DIFFRACTION98.97
4.72-5.090.25091560.19342973X-RAY DIFFRACTION98.12
5.09-5.60.2411590.20893020X-RAY DIFFRACTION98.54
5.6-6.410.2611610.22973055X-RAY DIFFRACTION99.69
6.41-8.070.24341610.20833053X-RAY DIFFRACTION99.5
8-46.640.22391630.20593122X-RAY DIFFRACTION98.77

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