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- PDB-4edf: Dimeric hUGDH, K94E -

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Basic information

Entry
Database: PDB / ID: 4edf
TitleDimeric hUGDH, K94E
ComponentsUDP-glucose 6-dehydrogenase
KeywordsOXIDOREDUCTASE / oligomeric state / molecular switch / medium chain dehydrogenase / glucuronidation / MDR / Rossmann fold
Function / homology
Function and homology information


Formation of the active cofactor, UDP-glucuronate / : / UDP-glucose 6-dehydrogenase / UDP-glucose 6-dehydrogenase activity / UDP-glucuronate biosynthetic process / glycosaminoglycan biosynthetic process / heparan sulfate proteoglycan biosynthetic process / gastrulation with mouth forming second / protein hexamerization / neuron development ...Formation of the active cofactor, UDP-glucuronate / : / UDP-glucose 6-dehydrogenase / UDP-glucose 6-dehydrogenase activity / UDP-glucuronate biosynthetic process / glycosaminoglycan biosynthetic process / heparan sulfate proteoglycan 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
URIDINE-5'-DIPHOSPHATE-GLUCOSE / UDP-glucose 6-dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsSennett, N.C. / Wood, Z.A.
CitationJournal: Biochemistry / Year: 2012
Title: Cofactor binding triggers a molecular switch to allosterically activate human UDP-{alpha}-D-glucose 6-dehydrogenase.
Authors: Sennett, N.C. / Kadirvelraj, R. / Wood, Z.A.
History
DepositionMar 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_ref_seq_dif / struct_site
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.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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
D: UDP-glucose 6-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,6418
Polymers220,3754
Non-polymers2,2654
Water2,648147
1
A: UDP-glucose 6-dehydrogenase
D: UDP-glucose 6-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,3204
Polymers110,1882
Non-polymers1,1332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7380 Å2
ΔGint-56 kcal/mol
Surface area32510 Å2
MethodPISA
2
B: UDP-glucose 6-dehydrogenase
C: UDP-glucose 6-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,3204
Polymers110,1882
Non-polymers1,1332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7420 Å2
ΔGint-56 kcal/mol
Surface area32390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.660, 151.070, 88.740
Angle α, β, γ (deg.)90.00, 107.01, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHESERSERchain 'A' and (resseq 2:88 or resseq 111:147 or resseq 153:381 or resseq 389:465 )AA2 - 882 - 88
12ALAALAASNASNchain 'A' and (resseq 2:88 or resseq 111:147 or resseq 153:381 or resseq 389:465 )AA111 - 147111 - 147
13ASNASNSERSERchain 'A' and (resseq 2:88 or resseq 111:147 or resseq 153:381 or resseq 389:465 )AA153 - 381153 - 381
14ASPASPLYSLYSchain 'A' and (resseq 2:88 or resseq 111:147 or resseq 153:381 or resseq 389:465 )AA389 - 465389 - 465
21PHEPHESERSERchain 'B' and (resseq 2:88 or resseq 111:147 or resseq 153:381 or resseq 389:465 )BB2 - 882 - 88
22ALAALAASNASNchain 'B' and (resseq 2:88 or resseq 111:147 or resseq 153:381 or resseq 389:465 )BB111 - 147111 - 147
23ASNASNSERSERchain 'B' and (resseq 2:88 or resseq 111:147 or resseq 153:381 or resseq 389:465 )BB153 - 381153 - 381
24ASPASPLYSLYSchain 'B' and (resseq 2:88 or resseq 111:147 or resseq 153:381 or resseq 389:465 )BB389 - 465389 - 465
31PHEPHESERSERchain 'C' and (resseq 2:88 or resseq 111:147 or resseq 153:381 or resseq 389:465 )CC2 - 882 - 88
32ALAALAASNASNchain 'C' and (resseq 2:88 or resseq 111:147 or resseq 153:381 or resseq 389:465 )CC111 - 147111 - 147
33ASNASNSERSERchain 'C' and (resseq 2:88 or resseq 111:147 or resseq 153:381 or resseq 389:465 )CC153 - 381153 - 381
34ASPASPLYSLYSchain 'C' and (resseq 2:88 or resseq 111:147 or resseq 153:381 or resseq 389:465 )CC389 - 465389 - 465
41PHEPHESERSERchain 'D' and (resseq 2:88 or resseq 111:147 or resseq 153:381 or resseq 389:465 )DD2 - 882 - 88
42ALAALAASNASNchain 'D' and (resseq 2:88 or resseq 111:147 or resseq 153:381 or resseq 389:465 )DD111 - 147111 - 147
43ASNASNSERSERchain 'D' and (resseq 2:88 or resseq 111:147 or resseq 153:381 or resseq 389:465 )DD153 - 381153 - 381
44ASPASPLYSLYSchain 'D' and (resseq 2:88 or resseq 111:147 or resseq 153:381 or resseq 389:465 )DD389 - 465389 - 465

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Components

#1: Protein
UDP-glucose 6-dehydrogenase / hUGDH / UDP-Glc dehydrogenase / UDP-GlcDH / UDPGDH


Mass: 55093.871 Da / Num. of mol.: 4 / Mutation: K94E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Gene ID. 7358, UGDH / Plasmid: pet15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O60701, UDP-glucose 6-dehydrogenase
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.58 Å3/Da / Density % sol: 52.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 5 mM UDP-glucose, 200 mM magnesium chloride, 100 mM citrate tribasic dihydrate, pH 5.0, 10% PEG20000, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 6, 2010
RadiationMonochromator: Rosenbaum-Rock double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: l,-k,h / Fraction: 0.329
ReflectionResolution: 2.08→50 Å / Num. all: 133637 / Num. obs: 131092 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rsym value: 0.077 / Net I/σ(I): 11.02
Reflection shellResolution: 2.08→2.21 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.58 / Num. unique all: 20643 / Rsym value: 0.472 / % possible all: 95.6

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Processing

Software
NameVersionClassification
SERGUISoftwaredata collection
MOLREPphasing
PHENIX(phenix.refine: dev_987)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Q3E

2q3e


Resolution: 2.08→43.306 Å / σ(F): 2 / Phase error: 31.76 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2374 6735 5.14 %RANDOM
Rwork0.1868 ---
all0.1922 133637 --
obs0.1868 131092 98.1 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.092 Å2 / ksol: 0.352 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.5124 Å2-0 Å2-0.2787 Å2
2--0.2813 Å2-0 Å2
3----0.7937 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: LAST / Resolution: 2.08→43.306 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13427 0 144 147 13718
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313808
X-RAY DIFFRACTIONf_angle_d0.73518686
X-RAY DIFFRACTIONf_dihedral_angle_d14.7135155
X-RAY DIFFRACTIONf_chiral_restr0.0492141
X-RAY DIFFRACTIONf_plane_restr0.0032380
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3374X-RAY DIFFRACTIONPOSITIONAL0.013
12B3374X-RAY DIFFRACTIONPOSITIONAL0.013
13C3326X-RAY DIFFRACTIONPOSITIONAL0.018
14D3337X-RAY DIFFRACTIONPOSITIONAL0.016
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.11590.30073070.28785923X-RAY DIFFRACTION88
2.1159-2.15440.29273250.28166253X-RAY DIFFRACTION94
2.1544-2.19580.29433520.27356171X-RAY DIFFRACTION93
2.1958-2.24060.30063130.26846247X-RAY DIFFRACTION94
2.2406-2.28940.25313430.27186180X-RAY DIFFRACTION93
2.2894-2.34260.26663170.26216304X-RAY DIFFRACTION94
2.3426-2.40120.27413310.25836255X-RAY DIFFRACTION94
2.4012-2.46610.27673370.25086203X-RAY DIFFRACTION93
2.4661-2.53860.27723220.25316246X-RAY DIFFRACTION94
2.5386-2.62050.26723150.25076227X-RAY DIFFRACTION94
2.6205-2.71410.26553610.25016221X-RAY DIFFRACTION93
2.7141-2.82270.26613230.23626217X-RAY DIFFRACTION94
2.8227-2.95110.24543260.22786304X-RAY DIFFRACTION94
2.9511-3.10660.24563110.22066245X-RAY DIFFRACTION94
3.1066-3.3010.23163350.21086246X-RAY DIFFRACTION93
3.301-3.55560.22013250.19546216X-RAY DIFFRACTION93
3.5556-3.91290.18533320.16356206X-RAY DIFFRACTION93
3.9129-4.47790.16983600.14516197X-RAY DIFFRACTION92
4.4779-5.63680.1613230.13936261X-RAY DIFFRACTION93
5.6368-32.43380.18123600.16226328X-RAY DIFFRACTION93

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