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- PDB-2o3j: Structure of Caenorhabditis Elegans UDP-Glucose Dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 2o3j
TitleStructure of Caenorhabditis Elegans UDP-Glucose Dehydrogenase
ComponentsUDP-glucose 6-dehydrogenase
KeywordsOXIDOREDUCTASE / UDP-GLUCOSE DEHYDROGENASE / STRUCTURAL GENOMICS / PSI-2 / PROTEIN STRUCTURE INITIATIVE / New York SGX Research Center for Structural Genomics / NYSGXRC
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 / Cytochrome c1, transmembrane anchor, C-terminal / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
UDP-glucose 6-dehydrogenase
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsZhang, Y. / Zhan, C. / Patskovsky, Y. / Ramagopal, U. / Shi, W. / Toro, R. / Wengerter, B.C. / Milst, S. / Vidal, M. / Burley, S.K. ...Zhang, Y. / Zhan, C. / Patskovsky, Y. / Ramagopal, U. / Shi, W. / Toro, R. / Wengerter, B.C. / Milst, S. / Vidal, M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of Caenorhabditis Elegans Udp-Glucose Dehydrogenase
Authors: Zhang, Y. / Zhan, C. / Patskovsky, Y. / Ramagopal, U. / Shi, W. / Toro, R. / Wengerter, B.C. / Milstein, S. / Vidal, M. / Burley, S.K. / Almo, S.C.
History
DepositionDec 1, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,26512
Polymers158,4363
Non-polymers8299
Water15,205844
1
A: UDP-glucose 6-dehydrogenase
B: UDP-glucose 6-dehydrogenase
C: UDP-glucose 6-dehydrogenase
hetero molecules

A: UDP-glucose 6-dehydrogenase
B: UDP-glucose 6-dehydrogenase
C: UDP-glucose 6-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)318,53024
Polymers316,8726
Non-polymers1,65818
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area28920 Å2
ΔGint-150 kcal/mol
Surface area101130 Å2
MethodPISA
2
A: UDP-glucose 6-dehydrogenase
C: UDP-glucose 6-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,1778
Polymers105,6242
Non-polymers5536
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
B: UDP-glucose 6-dehydrogenase
hetero molecules

B: UDP-glucose 6-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,1778
Polymers105,6242
Non-polymers5536
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)159.716, 144.092, 92.072
Angle α, β, γ (deg.)90.00, 123.24, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 6

Dom-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1ASPASPAA3 - 4713 - 471
2PHEPHEBB6 - 4716 - 471
3PHEPHECC6 - 4716 - 471

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Components

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


Mass: 52812.008 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Production host: Escherichia coli (E. coli) / References: UniProt: Q19905, UDP-glucose 6-dehydrogenase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 844 / 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: 2.8 Å3/Da / Density % sol: 56.14 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 200 MM MgCl2, 100 MM BIS-TRIS, PH 5.50, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 15, 2006 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. obs: 133254 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 34.4 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.057 / Net I/σ(I): 2.7
Reflection shellResolution: 1.88→1.95 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 0.8 / Num. unique all: 25057 / Rsym value: 0.71 / % possible all: 90.4

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1DLI

1dli


Resolution: 1.88→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.252 / SU ML: 0.126 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.148 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26315 4145 3 %RANDOM
Rwork0.20858 ---
obs0.2102 133254 98.17 %-
all-133254 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.475 Å2
Baniso -1Baniso -2Baniso -3
1--2.26 Å20 Å2-1.11 Å2
2--1.47 Å20 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 1.88→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10719 0 54 844 11617
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02211154
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1141.95415148
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.53451444
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.86624.375480
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.826151922
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6681563
X-RAY DIFFRACTIONr_chiral_restr0.1040.21733
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028350
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1740.35381
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.57665
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.51321
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1560.3107
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.540
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.87427162
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.026311332
X-RAY DIFFRACTIONr_scbond_it7.4234460
X-RAY DIFFRACTIONr_scangle_it9.90353785
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 3462 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional0.35
2Bloose positional0.315
3Cloose positional0.335
1Aloose thermal7.3610
2Bloose thermal6.8710
3Cloose thermal9.2610
LS refinement shellResolution: 1.88→1.932 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 268 -
Rwork0.316 8345 -
obs--84.65 %

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