[English] 日本語
Yorodumi
- PDB-2i6t: Orthorhombic Structure of the LDH domain of Human Ubiquitin-conju... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2i6t
TitleOrthorhombic Structure of the LDH domain of Human Ubiquitin-conjugating Enzyme E2-like Isoform A
ComponentsUBIQUITIN-CONJUGATING ENZYME E2-LIKE ISOFORM A
KeywordsUNKNOWN FUNCTION / L-lactate dehydrogenase / oxidoreductase / ubiquitin-protein ligase
Function / homology
Function and homology information


ESCRT I complex / carboxylic acid metabolic process / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / endosome to lysosome transport / ubiquitin binding / protein modification process / protein transport / extracellular exosome
Similarity search - Function
Ubiquitin E2 variant, N-terminal / UEV domain / UEV domain profile. / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain ...Ubiquitin E2 variant, N-terminal / UEV domain / UEV domain profile. / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / Ubiquitin-conjugating enzyme/RWD-like / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 variant 3 / Ubiquitin-conjugating enzyme E2 variant 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWalker, J.R. / Avvakumov, G.V. / Xue, S. / Newman, E.M. / Finerty Jr., P.J. / Butler-Cole, C. / Tempel, W. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. ...Walker, J.R. / Avvakumov, G.V. / Xue, S. / Newman, E.M. / Finerty Jr., P.J. / Butler-Cole, C. / Tempel, W. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S.
Citation
Journal: To be Published
Title: Structural Investigation into the L-lactate Dehydrogenase Domain of Human Ubiquitin-conjugating Enzyme E2-like Isoform A
Authors: Avvakumov, G.V. / Walker, J.R. / Xue, S. / Newman, E.M. / Finerty Jr., P.J. / Butler-Cole, C. / Tempel, W. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S.
#1: Journal: BIOCHIM.BIOPHYS.ACTA / Year: 2002
Title: Identification and characterization of UEV3, a human cDNA with similarities to inactive E2 ubiquitin-conjugating enzymes
Authors: Kloor, M. / Bork, P. / Duwe, A. / Klaes, R. / von Knebel Doeberitz, M. / Ridder, R.
History
DepositionAug 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 30, 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_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_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: UBIQUITIN-CONJUGATING ENZYME E2-LIKE ISOFORM A
B: UBIQUITIN-CONJUGATING ENZYME E2-LIKE ISOFORM A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,67213
Polymers65,6432
Non-polymers1,02911
Water4,990277
1
A: UBIQUITIN-CONJUGATING ENZYME E2-LIKE ISOFORM A
B: UBIQUITIN-CONJUGATING ENZYME E2-LIKE ISOFORM A
hetero molecules

A: UBIQUITIN-CONJUGATING ENZYME E2-LIKE ISOFORM A
B: UBIQUITIN-CONJUGATING ENZYME E2-LIKE ISOFORM A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,34326
Polymers131,2854
Non-polymers2,05822
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-77 kcal/mol
Surface area23080 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)53.088, 98.912, 126.753
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-506-

HOH

21B-601-

HOH

DetailsThe biological assembly is a tetramer generated by the two fold axis: -x, -y, z.

-
Components

#1: Protein UBIQUITIN-CONJUGATING ENZYME E2-LIKE ISOFORM A


Mass: 32821.367 Da / Num. of mol.: 2 / Fragment: L-lactate Dehydrogenase Domain, residues 171-471
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UEVLD / Plasmid: pET28-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6P2F0, UniProt: Q8IX04*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 2.53 Å3/Da / Density % sol: 51.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 26% PEG3350, 0.2 M ammonium sulfate, 0.1 M sodium cacodylate, pH 5.2 in protein buffer comprising of 20 mM Tris-HCl, pH 8.0, 500 mM NaCl, 5% glycerol, 10 mM dithiothreitol, VAPOR DIFFUSION, ...Details: 26% PEG3350, 0.2 M ammonium sulfate, 0.1 M sodium cacodylate, pH 5.2 in protein buffer comprising of 20 mM Tris-HCl, pH 8.0, 500 mM NaCl, 5% glycerol, 10 mM dithiothreitol, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 19, 2006
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.1→26.55 Å / Num. all: 39716 / Num. obs: 39716 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7 % / Rsym value: 0.18 / Net I/σ(I): 12.6
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 2.88 / Num. unique all: 3896 / Rsym value: 0.72 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1I10

1i10


Resolution: 2.1→26.55 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.134 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23004 2086 5.3 %RANDOM
Rwork0.18019 ---
obs0.18267 37628 99.82 %-
all-39715 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.562 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→26.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4281 0 62 277 4620
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224455
X-RAY DIFFRACTIONr_angle_refined_deg1.4121.9716032
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6765566
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.98525.824170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.20415807
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.0171514
X-RAY DIFFRACTIONr_chiral_restr0.0920.2736
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023154
X-RAY DIFFRACTIONr_nbd_refined0.2150.22141
X-RAY DIFFRACTIONr_nbtor_refined0.30.23046
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2310
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.2100
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.240
X-RAY DIFFRACTIONr_mcbond_it2.07732890
X-RAY DIFFRACTIONr_mcangle_it3.0744571
X-RAY DIFFRACTIONr_scbond_it4.02651746
X-RAY DIFFRACTIONr_scangle_it6.03771459
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 348 -
Rwork0.202 2539 -
obs--99.93 %

+
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