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- PDB-9gll: Crystal Structure of UFC1 T106L -

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Basic information

Entry
Database: PDB / ID: 9gll
TitleCrystal Structure of UFC1 T106L
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
Ubiquitin-fold modifier-conjugating enzyme 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 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


Theoretical massNumber of molelcules
Total (without water)19,6531
Polymers19,6531
Non-polymers00
Water2,738152
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)47.200, 47.200, 142.800
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-257-

HOH

21AAA-297-

HOH

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Components

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


Mass: 19652.598 Da / Num. of mol.: 1 / Mutation: T106L
Source method: isolated from a genetically manipulated source
Details: Threonine at 106th position is mutated to Leucine / Source: (gene. exp.) Homo sapiens (human) / Gene: UFC1, CGI-126, HSPC155 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y3C8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O
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: 2.02 Å3/Da / Density % sol: 39.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 1.4M Sodium potassium monobasic monohydrate/Potassium phosphate dibasic pH 9.0

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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: Dec 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.65→44.82 Å / Num. obs: 20255 / % possible obs: 99.58 % / Redundancy: 2 % / Biso Wilson estimate: 11.53 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.06703 / Net I/σ(I): 12.61
Reflection shellResolution: 1.65→1.709 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.61 / Num. unique obs: 1959 / CC1/2: 0.664 / Rrim(I) all: 0.594 / % possible all: 98.49

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→44.815 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.926 / SU B: 2.569 / SU ML: 0.084 / Cross valid method: FREE R-VALUE / ESU R: 0.119 / ESU R Free: 0.111
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.231 1031 5.091 %
Rwork0.203 19221 -
all0.204 --
obs-20252 99.577 %
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: 13.882 Å2
Baniso -1Baniso -2Baniso -3
1--0.423 Å20 Å20 Å2
2---0.423 Å20 Å2
3---0.845 Å2
Refinement stepCycle: LAST / Resolution: 1.65→44.815 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1352 0 0 152 1504
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0131469
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151373
X-RAY DIFFRACTIONr_angle_refined_deg1.681.6462003
X-RAY DIFFRACTIONr_angle_other_deg1.4291.5843174
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7895180
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.20522.02484
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.13215253
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6911511
X-RAY DIFFRACTIONr_chiral_restr0.0860.2182
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021687
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02351
X-RAY DIFFRACTIONr_nbd_refined0.2070.2292
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.21202
X-RAY DIFFRACTIONr_nbtor_refined0.1710.2696
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.2615
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.293
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1210.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2950.225
X-RAY DIFFRACTIONr_nbd_other0.2540.270
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3420.223
X-RAY DIFFRACTIONr_mcbond_it1.3251.266702
X-RAY DIFFRACTIONr_mcbond_other1.2451.261701
X-RAY DIFFRACTIONr_mcangle_it2.0581.885888
X-RAY DIFFRACTIONr_mcangle_other2.0631.889889
X-RAY DIFFRACTIONr_scbond_it2.0851.493767
X-RAY DIFFRACTIONr_scbond_other2.0741.493767
X-RAY DIFFRACTIONr_scangle_it3.2352.1371114
X-RAY DIFFRACTIONr_scangle_other3.2382.1381115
X-RAY DIFFRACTIONr_lrange_it5.33123.9076130
X-RAY DIFFRACTIONr_lrange_other4.99123.3635998
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.6930.29710.2861389X-RAY DIFFRACTION98.582
1.693-1.7390.259620.2591330X-RAY DIFFRACTION98.5836
1.739-1.7890.256850.2451299X-RAY DIFFRACTION99.2115
1.789-1.8440.313720.2321269X-RAY DIFFRACTION99.407
1.844-1.9050.226730.2261235X-RAY DIFFRACTION99.4677
1.905-1.9720.259610.221218X-RAY DIFFRACTION99.766
1.972-2.0460.278640.2091160X-RAY DIFFRACTION99.8369
2.046-2.1290.251680.1891113X-RAY DIFFRACTION99.9154
2.129-2.2240.196620.1721091X-RAY DIFFRACTION100
2.224-2.3320.222610.1871022X-RAY DIFFRACTION100
2.332-2.4580.18560.18998X-RAY DIFFRACTION100
2.458-2.6060.23410.181949X-RAY DIFFRACTION100
2.606-2.7860.274440.198915X-RAY DIFFRACTION99.8958
2.786-3.0080.231360.207834X-RAY DIFFRACTION100
3.008-3.2930.225370.205776X-RAY DIFFRACTION100
3.293-3.680.215370.195714X-RAY DIFFRACTION99.7344
3.68-4.2440.223330.168642X-RAY DIFFRACTION99.7046
4.244-5.1860.172360.166538X-RAY DIFFRACTION99.8261
5.186-7.2860.238160.201445X-RAY DIFFRACTION99.3534
7.286-44.8150.194160.222284X-RAY DIFFRACTION98.6842

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