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- PDB-9glk: Crystal Structure of UFC1 E149I -

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Basic information

Entry
Database: PDB / ID: 9glk
TitleCrystal Structure of UFC1 E149I
ComponentsUbiquitin-fold modifier-conjugating enzyme 1
KeywordsLIGASE / UFM1 conjugating enzyme1 / UBC core domain containing protein / Brain development / Infantile encephalopathy
Function / homology
Function and homology information


UFM1 conjugating enzyme activity / UFM1 transferase activity / protein K69-linked ufmylation / protein ufmylation / regulation of type II interferon production / reticulophagy / response to endoplasmic reticulum stress / brain development / extracellular exosome
Similarity search - Function
Ubiquitin-fold modifier-conjugating enzyme 1 / Ubiquitin-fold modifier-conjugating enzyme 1 / Ubiquitin-conjugating enzyme/RWD-like
Similarity search - Domain/homology
IMIDAZOLE / Ubiquitin-fold modifier-conjugating enzyme 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsKumar, M. / Banerjee, S. / Wiener, R.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation491/2021 Israel
CitationJournal: Nat Commun / Year: 2025
Title: UFC1 reveals the multifactorial and plastic nature of oxyanion holes in E2 conjugating enzymes.
Authors: Kumar, M. / Banerjee, S. / Cohen-Kfir, E. / Mitelberg, M.B. / Tiwari, S. / Isupov, M.N. / Dessau, M. / Wiener, R.
History
DepositionAug 27, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 7, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Ubiquitin-fold modifier-conjugating enzyme 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6942
Polymers19,6251
Non-polymers691
Water3,081171
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.300, 47.300, 143.270
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11AAA-372-

HOH

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Components

#1: Protein Ubiquitin-fold modifier-conjugating enzyme 1 / Ufm1-conjugating enzyme 1


Mass: 19624.588 Da / Num. of mol.: 1 / Mutation: E149I
Source method: isolated from a genetically manipulated source
Details: Glutamate at 149th position is mutated to Isoleucine
Source: (gene. exp.) Homo sapiens (human) / Gene: UFC1, CGI-126, HSPC155 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y3C8
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.04 Å3/Da / Density % sol: 39.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1M Bis-Tris pH 5.5, 2.0M Ammonium sulfate

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Aug 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2.03→39.47 Å / Num. obs: 19946 / % possible obs: 99.5 % / Redundancy: 3.38 % / Biso Wilson estimate: 19.32 Å2 / CC1/2: 0.973 / Rrim(I) all: 0.19 / Net I/σ(I): 10.38
Reflection shellResolution: 2.03→2.103 Å / Redundancy: 2.18 % / Mean I/σ(I) obs: 1.75 / Num. unique obs: 1471 / CC1/2: 0.49 / Rrim(I) all: 0.959 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
CootWinCoot 0.9.6 ELmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→39.47 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.901 / SU B: 5.701 / SU ML: 0.147 / Cross valid method: FREE R-VALUE / ESU R: 0.255 / ESU R Free: 0.195
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2471 564 5.039 %
Rwork0.2085 10629 -
all0.211 --
obs-11193 99.875 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 14.729 Å2
Baniso -1Baniso -2Baniso -3
1--0.643 Å20 Å20 Å2
2---0.643 Å20 Å2
3---1.286 Å2
Refinement stepCycle: LAST / Resolution: 2.03→39.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1345 0 5 171 1521
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131420
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151329
X-RAY DIFFRACTIONr_angle_refined_deg1.5711.6441930
X-RAY DIFFRACTIONr_angle_other_deg1.3341.5823068
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1815172
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.54322.56874
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.20815239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.181159
X-RAY DIFFRACTIONr_chiral_restr0.0780.2178
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021614
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02330
X-RAY DIFFRACTIONr_nbd_refined0.2020.2328
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2060.21214
X-RAY DIFFRACTIONr_nbtor_refined0.1670.2674
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.2577
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2128
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2360.220
X-RAY DIFFRACTIONr_nbd_other0.2320.275
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2550.222
X-RAY DIFFRACTIONr_mcbond_it1.0631.437682
X-RAY DIFFRACTIONr_mcbond_other1.0581.432681
X-RAY DIFFRACTIONr_mcangle_it1.6962.14856
X-RAY DIFFRACTIONr_mcangle_other1.6962.146857
X-RAY DIFFRACTIONr_scbond_it1.5351.532738
X-RAY DIFFRACTIONr_scbond_other1.5341.534739
X-RAY DIFFRACTIONr_scangle_it2.2982.2321074
X-RAY DIFFRACTIONr_scangle_other2.2972.2351075
X-RAY DIFFRACTIONr_lrange_it5.26417.8071718
X-RAY DIFFRACTIONr_lrange_other4.74417.1611677
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.0830.326360.27757X-RAY DIFFRACTION99.8741
2.083-2.140.246280.255761X-RAY DIFFRACTION100
2.14-2.2020.233410.233720X-RAY DIFFRACTION100
2.202-2.2690.445360.366699X-RAY DIFFRACTION99.0566
2.269-2.3430.284280.271688X-RAY DIFFRACTION99.7215
2.343-2.4250.272320.223661X-RAY DIFFRACTION100
2.425-2.5170.222330.207645X-RAY DIFFRACTION99.8527
2.517-2.6190.345370.206624X-RAY DIFFRACTION100
2.619-2.7350.243390.207576X-RAY DIFFRACTION100
2.735-2.8680.183270.183584X-RAY DIFFRACTION100
2.868-3.0230.22310.198551X-RAY DIFFRACTION100
3.023-3.2050.301340.203512X-RAY DIFFRACTION100
3.205-3.4250.218310.186495X-RAY DIFFRACTION100
3.425-3.6980.21310.182457X-RAY DIFFRACTION100
3.698-4.0480.224250.16425X-RAY DIFFRACTION100
4.048-4.5210.133170.133392X-RAY DIFFRACTION100
4.521-5.2120.254140.146367X-RAY DIFFRACTION99.7382
5.212-6.3620.171180.171304X-RAY DIFFRACTION100
6.362-8.9080.239160.174249X-RAY DIFFRACTION100
8.908-39.470.319100.205162X-RAY DIFFRACTION99.422

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