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- PDB-6om8: Caenorhabditis Elegans UDP-Glucose Dehydrogenase in complex with ... -

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Basic information

Entry
Database: PDB / ID: 6om8
TitleCaenorhabditis Elegans UDP-Glucose Dehydrogenase in complex with UDP-Xylose
ComponentsUDP-glucose 6-dehydrogenase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Dehydrogenase / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


Formation of the active cofactor, UDP-glucuronate / vulval development / egg-laying behavior / UDP-glucose 6-dehydrogenase / UDP-glucose 6-dehydrogenase activity / : / UDP-glucuronate biosynthetic process / glycosaminoglycan biosynthetic process / embryo development ending in birth or egg hatching / morphogenesis of an epithelium ...Formation of the active cofactor, UDP-glucuronate / vulval development / egg-laying behavior / UDP-glucose 6-dehydrogenase / UDP-glucose 6-dehydrogenase activity / : / UDP-glucuronate biosynthetic process / glycosaminoglycan biosynthetic process / embryo development ending in birth or egg hatching / morphogenesis of an epithelium / NAD binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
UDP-glucose 6-dehydrogenase, eukaryotic type / UDP-glucose/GDP-mannose dehydrogenase, N-terminal / UDP-glucose/GDP-mannose dehydrogenase, dimerisation / UDP-glucose/GDP-mannose dehydrogenase, C-terminal / UDP-glucose/GDP-mannose dehydrogenase / UDP-glucose/GDP-mannose dehydrogenase, C-terminal domain superfamily / UDP-glucose/GDP-mannose dehydrogenase family, central domain / UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain / UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain / UDP binding domain ...UDP-glucose 6-dehydrogenase, eukaryotic type / UDP-glucose/GDP-mannose dehydrogenase, N-terminal / UDP-glucose/GDP-mannose dehydrogenase, dimerisation / UDP-glucose/GDP-mannose dehydrogenase, C-terminal / UDP-glucose/GDP-mannose dehydrogenase / UDP-glucose/GDP-mannose dehydrogenase, C-terminal domain superfamily / UDP-glucose/GDP-mannose dehydrogenase family, central domain / UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain / UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain / UDP binding domain / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE / UDP-glucose 6-dehydrogenase
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.449 Å
AuthorsBeattie, N.R. / McDonald, W.E. / Hicks Sirmans, T.N. / Wood, Z.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM11429 United States
CitationJournal: Acs Omega / Year: 2019
Title: Conservation of Atypical Allostery inC. elegansUDP-Glucose Dehydrogenase.
Authors: Beattie, N.R. / Keul, N.D. / Hicks Sirmans, T.N. / McDonald, W.E. / Talmadge, T.M. / Taujale, R. / Kannan, N. / Wood, Z.A.
History
DepositionApr 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-glucose 6-dehydrogenase
B: UDP-glucose 6-dehydrogenase
C: UDP-glucose 6-dehydrogenase
D: UDP-glucose 6-dehydrogenase
E: UDP-glucose 6-dehydrogenase
F: UDP-glucose 6-dehydrogenase
G: UDP-glucose 6-dehydrogenase
H: UDP-glucose 6-dehydrogenase
I: UDP-glucose 6-dehydrogenase
J: UDP-glucose 6-dehydrogenase
K: UDP-glucose 6-dehydrogenase
L: UDP-glucose 6-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)646,61536
Polymers633,74412
Non-polymers12,87124
Water21,5101194
1
A: UDP-glucose 6-dehydrogenase
B: UDP-glucose 6-dehydrogenase
C: UDP-glucose 6-dehydrogenase
D: UDP-glucose 6-dehydrogenase
E: UDP-glucose 6-dehydrogenase
F: UDP-glucose 6-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)323,30718
Polymers316,8726
Non-polymers6,43512
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33570 Å2
ΔGint-231 kcal/mol
Surface area99880 Å2
MethodPISA
2
G: UDP-glucose 6-dehydrogenase
H: UDP-glucose 6-dehydrogenase
hetero molecules

K: UDP-glucose 6-dehydrogenase
L: UDP-glucose 6-dehydrogenase
hetero molecules

I: UDP-glucose 6-dehydrogenase
J: UDP-glucose 6-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)323,30718
Polymers316,8726
Non-polymers6,43512
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation4_855-x+3,-y+1/2,z+1/21
Buried area33570 Å2
ΔGint-238 kcal/mol
Surface area99380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.710, 168.170, 279.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein
UDP-glucose 6-dehydrogenase / / UDPGDH / Squashed vulva protein 4


Mass: 52812.008 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: sqv-4, F29F11.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q19905, UDP-glucose 6-dehydrogenase
#2: Chemical...
ChemComp-UDX / URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE / UDP-ALPHA-D-XYLOPYRANOSE


Mass: 536.276 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C14H22N2O16P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1194 / Source method: isolated from a natural source / Formula: H2O

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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: 3.04 Å3/Da / Density % sol: 59.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 10 mg/mL C. Elegans UDP-Glucose Dehydrogenase Citric acid buffer pH 5.0 200mM Lithium Chloride 4% PEG 8000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.449→52.698 Å / Num. obs: 266791 / % possible obs: 98.1 % / Redundancy: 6.295 % / CC1/2: 0.996 / Net I/σ(I): 9.1
Reflection shellResolution: 2.449→2.51 Å / Num. unique obs: 19914 / CC1/2: 0.455

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
XDSdata scaling
Cootmodel building
PHENIXphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O3J

2o3j


Resolution: 2.449→52.698 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.68
RfactorNum. reflection% reflection
Rfree0.2204 1847 0.69 %
Rwork0.1935 --
obs0.1937 266577 98.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.449→52.698 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms42852 0 816 1194 44862
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00844629
X-RAY DIFFRACTIONf_angle_d0.91160708
X-RAY DIFFRACTIONf_dihedral_angle_d21.43216456
X-RAY DIFFRACTIONf_chiral_restr0.0637019
X-RAY DIFFRACTIONf_plane_restr0.0057690
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4494-2.51560.3381420.30720176X-RAY DIFFRACTION98
2.5156-2.58960.38461430.296520686X-RAY DIFFRACTION100
2.5896-2.67320.31851390.283320553X-RAY DIFFRACTION100
2.6732-2.76870.29741470.262520578X-RAY DIFFRACTION100
2.7687-2.87960.28681460.25320566X-RAY DIFFRACTION100
2.8796-3.01060.25341250.24420553X-RAY DIFFRACTION100
3.0106-3.16930.2671620.235320490X-RAY DIFFRACTION99
3.1693-3.36790.24081430.228920406X-RAY DIFFRACTION99
3.3679-3.62780.21011420.203320230X-RAY DIFFRACTION98
3.6278-3.99280.26211340.184220092X-RAY DIFFRACTION97
3.9928-4.57030.17771450.152820027X-RAY DIFFRACTION96
4.5703-5.7570.18331410.149220052X-RAY DIFFRACTION96
5.757-52.71040.14611380.14220321X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: 180.3146 Å / Origin y: 40.7553 Å / Origin z: 77.4531 Å
111213212223313233
T0.3494 Å2-0.0339 Å20.0128 Å2-0.3146 Å2-0.0147 Å2--0.3784 Å2
L0.0084 °2-0.0083 °2-0.0204 °2-0.0547 °20.0092 °2--0.1779 °2
S-0.0059 Å °-0.0024 Å °-0.0143 Å °-0.0138 Å °-0.0059 Å °-0.0379 Å °-0.0249 Å °0.0144 Å °0.0119 Å °
Refinement TLS groupSelection details: all

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