[English] 日本語
Yorodumi
- PDB-4edf: Dimeric hUGDH, K94E -

+
Open data


ID or keywords:

Loading...

-
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 / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more