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- PDB-2i6t: Orthorhombic Structure of the LDH domain of Human Ubiquitin-conju... -

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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 / protein modification process => GO:0036211 / lactate metabolic process / carboxylic acid metabolic process / L-lactate dehydrogenase activity / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / pyruvate metabolic process / endosome to lysosome transport / ubiquitin binding / protein modification process ...ESCRT I complex / protein modification process => GO:0036211 / lactate metabolic process / carboxylic acid metabolic process / L-lactate dehydrogenase activity / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / pyruvate metabolic process / endosome to lysosome transport / ubiquitin binding / protein modification process / protein transport / carbohydrate metabolic process / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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.

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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

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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: 2.53 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

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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

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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 %

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