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- PDB-5w4x: Truncated hUGDH -

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Basic information

Entry
Database: PDB / ID: 5w4x
TitleTruncated hUGDH
ComponentsUDP-glucose 6-dehydrogenase
KeywordsOXIDOREDUCTASE / DEHYDROGENASE / UDP-SUGAR BINDING / UDP-GLUCURONIC ACID / ROSSMANN FOLD / OXIDATION / CYTOSOL
Function / homology
Function and homology information


Formation of the active cofactor, UDP-glucuronate / chondroitin sulfate biosynthetic process / UDP-glucose 6-dehydrogenase / UDP-glucose 6-dehydrogenase activity / UDP-glucuronate biosynthetic process / heparan sulfate proteoglycan biosynthetic process / glycosaminoglycan biosynthetic process / gastrulation with mouth forming second / protein hexamerization / neuron development ...Formation of the active cofactor, UDP-glucuronate / chondroitin sulfate biosynthetic process / UDP-glucose 6-dehydrogenase / UDP-glucose 6-dehydrogenase activity / UDP-glucuronate biosynthetic process / heparan sulfate proteoglycan biosynthetic process / glycosaminoglycan biosynthetic process / gastrulation with mouth forming second / protein hexamerization / neuron development / NAD binding / carbohydrate metabolic process / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytosol
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
1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / UDP-glucose 6-dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsSennett, N.C. / Custer, G.S. / Wood, Z.A.
CitationJournal: Nature / Year: 2018
Title: The entropic force generated by intrinsically disordered segments tunes protein function.
Authors: Keul, N.D. / Oruganty, K. / Schaper Bergman, E.T. / Beattie, N.R. / McDonald, W.E. / Kadirvelraj, R. / Gross, M.L. / Phillips, R.S. / Harvey, S.C. / Wood, Z.A.
History
DepositionJun 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
SupersessionOct 18, 2017ID: 4QEJ
Revision 2.0Oct 18, 2017Group: Advisory / Data collection ...Advisory / Data collection / Database references / Polymer sequence / Source and taxonomy / Structure summary
Category: diffrn_radiation_wavelength / entity ...diffrn_radiation_wavelength / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_database_PDB_obs_spr / pdbx_unobs_or_zero_occ_residues / struct_ref / struct_ref_seq
Item: _diffrn_radiation_wavelength.wavelength / _entity.formula_weight ..._diffrn_radiation_wavelength.wavelength / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end
Revision 2.1Nov 14, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 2.2Nov 28, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 2.3Dec 5, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,5246
Polymers155,9893
Non-polymers5353
Water64936
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)313,04712
Polymers311,9786
Non-polymers1,0696
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area27700 Å2
ΔGint-118 kcal/mol
Surface area101150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.190, 114.066, 97.239
Angle α, β, γ (deg.)90.00, 116.85, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein UDP-glucose 6-dehydrogenase / / UDPGDH


Mass: 51996.340 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UGDH / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21T1R / References: UniProt: O60701, UDP-glucose 6-dehydrogenase
#2: Chemical ChemComp-PG5 / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / Triethylene glycol dimethyl ether


Mass: 178.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.67 Å3/Da / Density % sol: 53.88 %
Crystal growTemperature: 298 K / Method: liquid diffusion / pH: 6.2
Details: 1.0 MM CAPILLARY,5 L OF 10.4 MG/ML ENZYME AND 200 L OF 100 MM MES PH 6.2, 100 MM MGCL2, AND 16% PEG 3350
PH range: 6.2

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Aug 21, 2011
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.64→50 Å / Num. obs: 50632 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Biso Wilson estimate: 66.08 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.066 / Net I/σ(I): 21.98
Reflection shellResolution: 2.64→2.81 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 2.02 / Rsym value: 0.97 / % possible all: 99

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHASERphasing
PHENIX1.8.1_1156refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→35.83 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 26.49
RfactorNum. reflection% reflection
Rfree0.234 1981 3.93 %
Rwork0.187 --
obs0.189 50399 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.65→35.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10818 0 33 36 10887
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411043
X-RAY DIFFRACTIONf_angle_d0.75414926
X-RAY DIFFRACTIONf_dihedral_angle_d12.1434127
X-RAY DIFFRACTIONf_chiral_restr0.0561698
X-RAY DIFFRACTIONf_plane_restr0.0031921
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.71630.32721410.31033454X-RAY DIFFRACTION100
2.7163-2.78970.33031400.28633430X-RAY DIFFRACTION100
2.7897-2.87170.33121370.2723432X-RAY DIFFRACTION100
2.8717-2.96440.28471450.25133458X-RAY DIFFRACTION100
2.9644-3.07030.27471410.2453451X-RAY DIFFRACTION100
3.0703-3.19310.30141370.23043415X-RAY DIFFRACTION100
3.1931-3.33830.28071480.22943472X-RAY DIFFRACTION100
3.3383-3.51420.29891390.22213455X-RAY DIFFRACTION100
3.5142-3.73420.23961410.19143441X-RAY DIFFRACTION100
3.7342-4.02210.23661430.17173465X-RAY DIFFRACTION100
4.0221-4.42620.19791380.15383466X-RAY DIFFRACTION100
4.4262-5.06520.16761450.13963460X-RAY DIFFRACTION100
5.0652-6.37570.21061420.17583485X-RAY DIFFRACTION100
6.3757-35.8360.21171440.16193534X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.42911.38130.45643.74481.59063.23380.3598-0.3351-0.29020.9101-0.30470.08670.1568-1.115-0.03941.80980.30890.02141.32720.10250.6343-2.7722-5.614555.1178
22.29822.16673.1442.09492.88184.322-0.614-0.7081-0.44621.22870.61990.4453-0.7206-0.62630.04251.41230.45790.03220.99030.08660.5628-2.29725.630439.0749
32.8995-0.32110.51834.86082.49483.7271-0.0433-0.4069-0.06720.838-0.1109-0.323-0.46840.02380.181.37430.2711-0.1610.8780.01210.577510.5648-0.032945.8777
41.97550.8984-0.20412.5534-0.30891.9189-0.361-0.2949-0.07810.40370.17990.02450.4298-0.23120.15850.74290.18370.11540.53840.07460.4521-1.527-17.551222.1243
54.6037-0.81831.89332.74690.23115.1077-0.0776-0.94040.00950.48750.17130.39050.1627-1.3791-0.05861.2497-0.02330.32421.09510.14840.6595-19.9595-25.044925.7561
64.41242.12310.89484.0074-1.10092.71510.1065-0.2474-0.8530.3095-0.0171-0.31491.5249-0.1848-0.03271.5498-0.07370.39120.72390.18660.9365-8.9435-38.26820.391
71.97161.242-0.9784.4008-0.22842.13160.04710.03640.59250.04930.05660.8492-0.6368-0.646-0.10460.70330.2358-0.2040.80620.11860.9428-29.079237.8251-7.4446
81.4055-0.6335-0.32362.7019-0.37883.7571-0.3749-0.40960.14420.83560.40240.3479-0.4581-0.3349-0.01470.63410.2051-0.02690.51240.00150.5872-8.732426.611316.7693
92.0056-0.9980.94192.39480.47112.5456-0.17970.5332-0.52970.04360.0960.79530.5638-1.0260.23961.227-0.52330.30121.1745-0.09841.2437-39.3995-37.0486-11.1455
101.11370.1224-0.10711.81770.311.5969-0.2531-0.0876-0.44090.202-0.04090.32981.0674-0.62390.12791.2781-0.35740.260.7047-0.0190.9092-23.344-34.246-2.0614
111.08871.1137-0.30952.10750.7731.1672-0.35690.3047-0.328-0.35760.10740.65450.7131-0.40390.18891.018-0.40450.08890.7301-0.11280.7467-20.2537-24.1149-22.1433
122.231-0.9013-0.13953.2830.24981.5265-0.17780.23710.0688-0.50920.01161.03140.1103-0.69890.12950.5298-0.2162-0.19210.7656-0.03240.8441-30.72280.0657-14.8576
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 87 )
2X-RAY DIFFRACTION2chain 'A' and (resid 88 through 135 )
3X-RAY DIFFRACTION3chain 'A' and (resid 136 through 212 )
4X-RAY DIFFRACTION4chain 'A' and (resid 213 through 372 )
5X-RAY DIFFRACTION5chain 'A' and (resid 373 through 417 )
6X-RAY DIFFRACTION6chain 'A' and (resid 418 through 466 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 204 )
8X-RAY DIFFRACTION8chain 'B' and (resid 205 through 466 )
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 87 )
10X-RAY DIFFRACTION10chain 'C' and (resid 88 through 167 )
11X-RAY DIFFRACTION11chain 'C' and (resid 168 through 276 )
12X-RAY DIFFRACTION12chain 'C' and (resid 277 through 466 )

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