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- PDB-8wxk: Crystal Structure of UDP-Glucose 4-Epimerase (all4713) with UDP-g... -

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Basic information

Entry
Database: PDB / ID: 8wxk
TitleCrystal Structure of UDP-Glucose 4-Epimerase (all4713) with UDP-glucose and NAD from Nostoc sp. PCC 7120
ComponentsUDP-glucose 4-epimerase
KeywordsISOMERASE / UDP-Glucose 4-Epimerase (all4713) / UDP-glucose / NAD
Function / homology
Function and homology information


UDP-glucose 4-epimerase / UDP-glucose 4-epimerase activity / galactose metabolic process
Similarity search - Function
UDP-glucose 4-epimerase / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / URIDINE-5'-DIPHOSPHATE-GLUCOSE / UDP-glucose 4-epimerase
Similarity search - Component
Biological speciesNostoc sp. PCC 7120 = FACHB-418 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsSu, J.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171255 China
CitationJournal: To Be Published
Title: Crystal Structure of UDP-Glucose 4-Epimerase (all4713) with UDP-glucose and NAD from Nostoc sp. PCC 7120
Authors: Su, J.Y.
History
DepositionOct 30, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 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: UDP-glucose 4-epimerase
B: UDP-glucose 4-epimerase
C: UDP-glucose 4-epimerase
D: UDP-glucose 4-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,58412
Polymers145,6664
Non-polymers4,9198
Water5,332296
1
A: UDP-glucose 4-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6463
Polymers36,4161
Non-polymers1,2302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-12 kcal/mol
Surface area13470 Å2
MethodPISA
2
B: UDP-glucose 4-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6463
Polymers36,4161
Non-polymers1,2302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-11 kcal/mol
Surface area13090 Å2
MethodPISA
3
C: UDP-glucose 4-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6463
Polymers36,4161
Non-polymers1,2302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-13 kcal/mol
Surface area12970 Å2
MethodPISA
4
D: UDP-glucose 4-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6463
Polymers36,4161
Non-polymers1,2302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-11 kcal/mol
Surface area13140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.160, 101.490, 167.590
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
UDP-glucose 4-epimerase


Mass: 36416.383 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
Gene: all4713 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YN57
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H24N2O17P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.69 Å3/Da / Density % sol: 54.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.26→39.27 Å / Num. obs: 74297 / % possible obs: 100 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 18.5
Reflection shellResolution: 2.26→2.32 Å / Rmerge(I) obs: 1.346 / Num. unique obs: 5403

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Processing

SoftwareName: PHENIX / Version: (1.18.2_3874: ???) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.26→39.27 Å / SU ML: 0.27 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 24.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.229 2000 2.69 %
Rwork0.1823 --
obs0.1836 74215 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.26→39.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10533 0 0 296 10829
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910880
X-RAY DIFFRACTIONf_angle_d1.19314860
X-RAY DIFFRACTIONf_dihedral_angle_d12.2281484
X-RAY DIFFRACTIONf_chiral_restr0.0611664
X-RAY DIFFRACTIONf_plane_restr0.0071880
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.320.35821400.26075079X-RAY DIFFRACTION100
2.32-2.380.3541410.24915087X-RAY DIFFRACTION100
2.38-2.450.29511420.23935109X-RAY DIFFRACTION100
2.45-2.530.26751410.22535071X-RAY DIFFRACTION100
2.53-2.620.27351410.22285137X-RAY DIFFRACTION100
2.62-2.720.2941420.2285104X-RAY DIFFRACTION100
2.72-2.850.23381420.21895143X-RAY DIFFRACTION100
2.85-30.26171430.21275139X-RAY DIFFRACTION100
3-3.180.27281420.21325146X-RAY DIFFRACTION100
3.19-3.430.26141430.2125145X-RAY DIFFRACTION100
3.43-3.780.23991430.18235173X-RAY DIFFRACTION100
3.78-4.320.18461430.15635181X-RAY DIFFRACTION100
4.32-5.440.17851470.14365270X-RAY DIFFRACTION100
5.44-39.270.18731500.14185431X-RAY DIFFRACTION100

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