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- PDB-6c4k: Full length hUGDH with A104L substitution in the absence of ligand -

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Basic information

Entry
Database: PDB / ID: 6c4k
TitleFull length hUGDH with A104L substitution in the absence of ligand
ComponentsUDP-glucose 6-dehydrogenase
KeywordsOXIDOREDUCTASE / hUGDH / human UDP-Glucose Dehydrogenase
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 / 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
PHOSPHATE ION / UDP-glucose 6-dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsBeattie, N.R. / Pioso, B.J. / Wood, Z.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM114298 United States
CitationJournal: Biochemistry / Year: 2018
Title: Hysteresis and Allostery in Human UDP-Glucose Dehydrogenase Require a Flexible Protein Core.
Authors: Beattie, N.R. / Pioso, B.J. / Sidlo, A.M. / Keul, N.D. / Wood, Z.A.
History
DepositionJan 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 5, 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.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Dec 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,7167
Polymers165,4083
Non-polymers3084
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-49 kcal/mol
Surface area59780 Å2
MethodPISA
2
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)331,43214
Polymers330,8166
Non-polymers6168
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area26470 Å2
ΔGint-236 kcal/mol
Surface area102890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.520, 114.470, 96.880
Angle α, β, γ (deg.)90.00, 116.50, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-628-

HOH

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Components

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


Mass: 55136.020 Da / Num. of mol.: 3 / Mutation: A104L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UGDH / Production host: Escherichia coli (E. coli) / References: UniProt: O60701, UDP-glucose 6-dehydrogenase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.68 Å3/Da / Density % sol: 54.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6 / Details: 16% PEG 3350, 0.5M NaCl, 0.1M Tris (pH 7.6)

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARRESEARCH / 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: 2.65→48.161 Å / Num. obs: 50717 / % possible obs: 99.7 % / Redundancy: 7.7 % / Net I/σ(I): 13.73
Reflection shellResolution: 2.65→2.7116 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
Cootmodel building
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RJT

4rjt


Resolution: 2.65→48.161 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.97
RfactorNum. reflection% reflection
Rfree0.255 2147 4.24 %
Rwork0.2217 --
obs0.2232 50678 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.65→48.161 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10799 0 16 69 10884
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211015
X-RAY DIFFRACTIONf_angle_d0.42914901
X-RAY DIFFRACTIONf_dihedral_angle_d12.1284105
X-RAY DIFFRACTIONf_chiral_restr0.0411700
X-RAY DIFFRACTIONf_plane_restr0.0031916
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.71160.42541390.37023235X-RAY DIFFRACTION100
2.7116-2.77940.38071520.36253216X-RAY DIFFRACTION100
2.7794-2.85460.42071330.39193225X-RAY DIFFRACTION100
2.8546-2.93860.48731450.35593220X-RAY DIFFRACTION100
2.9386-3.03340.33981440.32953213X-RAY DIFFRACTION100
3.0334-3.14180.31211390.29263196X-RAY DIFFRACTION100
3.1418-3.26760.37031420.30053239X-RAY DIFFRACTION100
3.2676-3.41620.32351480.2843224X-RAY DIFFRACTION100
3.4162-3.59630.32861360.27073235X-RAY DIFFRACTION100
3.5963-3.82150.24991480.21933223X-RAY DIFFRACTION100
3.8215-4.11650.23631430.23235X-RAY DIFFRACTION100
4.1165-4.53040.21651430.17843238X-RAY DIFFRACTION100
4.5304-5.18530.19881450.16333277X-RAY DIFFRACTION100
5.1853-6.53040.2441420.20183259X-RAY DIFFRACTION100
6.5304-48.16850.17781480.16933296X-RAY DIFFRACTION99
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)
12.47451.58030.39394.79650.84485.6144-0.1202-0.7298-0.20581.6184-0.1351-0.06660.6027-0.99240.23741.99620.59520.0251.33250.13040.7506-2.4881-5.531255.2264
22.49920.40150.4910.1283-0.39234.2655-0.4109-0.2107-0.15870.97460.2961-0.1155-0.4341-0.22250.06211.58570.5559-0.21350.92450.07840.69445.69112.081243.3572
32.41020.73650.04052.5764-0.41972.4819-0.5904-0.3368-0.33530.45730.24210.03781.0756-0.44670.23161.13950.12450.34860.68460.08660.6132-6.0184-23.174322.2814
43.53241.54870.83482.2809-2.09774.67320.57160.15051.03640.1460.24561.6036-1.0666-1.2458-0.59061.2330.5732-0.10471.23110.18091.5887-33.76643.9496-1.2929
53.1207-0.08381.32120.05980.18891.4764-0.03150.4693-0.4496-0.31790.26311.1252-0.4101-0.7967-0.07790.72340.3045-0.3791.29460.21471.2207-28.658527.1031-10.7205
64.83291.08711.21681.44051.82472.74380.02480.36560.2215-0.23860.42670.5119-0.6833-0.6566-0.23211.15530.248-0.48040.94620.25741.1083-20.939741.5921-12.5658
73.9891-1.0680.65672.7896-1.35555.1776-0.4109-0.25240.32290.16010.29630.0817-0.9771-0.09360.11110.62880.0969-0.29690.4743-0.01780.6989-2.089931.37365.334
82.0918-1.0986-1.30223.67660.40275.1087-0.548-0.2725-0.11980.72350.42450.6373-0.1393-0.48710.13080.49810.2002-0.0990.6230.04520.75-11.131620.745814.2891
94.4387-0.05430.11485.79060.87234.073-0.3925-0.2842-0.26291.38890.44881.429-0.4182-1.07590.01241.11950.58150.23711.11050.21760.97-19.215823.709827.6116
101.85080.9075-1.30493.34660.4829.0008-0.7901-0.95830.18681.6690.67460.0431-1.32320.60860.07471.36730.4965-0.20290.9617-0.10040.757-2.412730.628131.4745
112.89471.59780.90022.75110.4390.5769-0.0211-0.1801-0.0537-0.2879-0.16210.7680.8999-0.86940.11991.5711-0.76910.23811.3415-0.13961.3457-36.0064-34.3593-7.9466
121.4160.60110.37231.50170.21710.6085-0.3970.2426-0.3858-0.23750.07980.36680.9363-0.4264-0.5112.0409-0.7570.43450.9101-0.17191.2165-23.4009-38.9436-12.1056
131.3949-0.5136-0.17581.8331-0.33432.0888-0.44770.137-0.0253-0.54610.19250.87380.6088-0.88810.15370.6127-0.388-0.13640.9136-0.11470.994-22.387-7.3404-15.6174
143.1767-1.0760.57220.77830.50651.2913-0.12260.3277-0.1681-0.4078-0.06170.95920.2401-1.13750.20320.7619-0.3625-0.53311.5940.02341.4901-36.82064.818-19.5406
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 87 )
2X-RAY DIFFRACTION2chain 'A' and (resid 88 through 212 )
3X-RAY DIFFRACTION3chain 'A' and (resid 213 through 466 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 81 )
5X-RAY DIFFRACTION5chain 'B' and (resid 82 through 146 )
6X-RAY DIFFRACTION6chain 'B' and (resid 147 through 212 )
7X-RAY DIFFRACTION7chain 'B' and (resid 213 through 276 )
8X-RAY DIFFRACTION8chain 'B' and (resid 277 through 372 )
9X-RAY DIFFRACTION9chain 'B' and (resid 373 through 417 )
10X-RAY DIFFRACTION10chain 'B' and (resid 418 through 468 )
11X-RAY DIFFRACTION11chain 'C' and (resid 1 through 116 )
12X-RAY DIFFRACTION12chain 'C' and (resid 117 through 212 )
13X-RAY DIFFRACTION13chain 'C' and (resid 213 through 372 )
14X-RAY DIFFRACTION14chain 'C' and (resid 373 through 466 )

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