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- PDB-3evx: Crystal structure of the human E2-like ubiquitin-fold modifier co... -

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Basic information

Entry
Database: PDB / ID: 3evx
TitleCrystal structure of the human E2-like ubiquitin-fold modifier conjugating enzyme 1 (Ufc1). Northeast Structural Genomics Consortium target HR41
ComponentsUfm1-conjugating enzyme 1
KeywordsLIGASE / alpha-beta protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Polymorphism / Ubl conjugation pathway
Function / homology
Function and homology information


UFM1 conjugating enzyme activity / UFM1 transferase activity / protein ufmylation / protein K69-linked ufmylation / 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 / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme/RWD-like / Roll / Alpha Beta
Similarity search - Domain/homology
THIOCYANATE ION / Ubiquitin-fold modifier-conjugating enzyme 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.54 Å
AuthorsForouhar, F. / Abashidze, M. / Seetharaman, J. / Ho, C.K. / Janjua, H. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Baran, M.C. / Acton, T.B. ...Forouhar, F. / Abashidze, M. / Seetharaman, J. / Ho, C.K. / Janjua, H. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: J.STRUCT.FUNCT.GENOM. / Year: 2009
Title: NMR and X-RAY structures of human E2-like ubiquitin-fold modifier conjugating enzyme 1 (UFC1) reveal structural and functional conservation in the metazoan UFM1-UBA5-UFC1 ubiquination pathway.
Authors: Liu, G. / Forouhar, F. / Eletsky, A. / Atreya, H.S. / Aramini, J.M. / Xiao, R. / Huang, Y.J. / Abashidze, M. / Seetharaman, J. / Liu, J. / Rost, B. / Acton, T. / Montelione, G.T. / Hunt, J.F. / Szyperski, T.
History
DepositionOct 13, 2008Deposition site: RCSB / Processing site: RCSB
SupersessionOct 21, 2008ID: 2IN1, 3E2G
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Jan 4, 2023Group: Database references / Derived calculations / Structure summary
Category: audit_author / database_2 ...audit_author / database_2 / struct_conn / struct_site
Item: _audit_author.name / _database_2.pdbx_DOI ..._audit_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: Ufm1-conjugating enzyme 1
B: Ufm1-conjugating enzyme 1
C: Ufm1-conjugating enzyme 1
D: Ufm1-conjugating enzyme 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,0258
Polymers82,7934
Non-polymers2324
Water3,045169
1
A: Ufm1-conjugating enzyme 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7562
Polymers20,6981
Non-polymers581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ufm1-conjugating enzyme 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7562
Polymers20,6981
Non-polymers581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ufm1-conjugating enzyme 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7562
Polymers20,6981
Non-polymers581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Ufm1-conjugating enzyme 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7562
Polymers20,6981
Non-polymers581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.368, 64.537, 66.422
Angle α, β, γ (deg.)90.06, 89.95, 105.18
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 20698.234 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CGI-126, HSPC155, UFC1 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q9Y3C8
#2: Chemical
ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CNS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, and 5 mM DTT. Reservoir solution:100mM Sodium acetate, 18% PEG8000, 100mM (NH4)SCN, 50mM LiSCN, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97898 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 10, 2007 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97898 Å / Relative weight: 1
ReflectionResolution: 2.54→30 Å / Num. all: 23056 / Num. obs: 22065 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.066 / Net I/σ(I): 14.11
Reflection shellResolution: 2.54→2.64 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.198 / Mean I/σ(I) obs: 5.8 / Num. unique all: 2496 / Rsym value: 0.149 / % possible all: 97.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SnBthen SOLVE/RESOLVEphasing
CNS1.2 & XtalViewrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.54→19.96 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 77510.06 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
Details: This crystal structure was initially refined in spacegroup P2(1), which gave canonical merging statistics during data processing that were very similar to those obtained in the lower ...Details: This crystal structure was initially refined in spacegroup P2(1), which gave canonical merging statistics during data processing that were very similar to those obtained in the lower symmetry spacegroup P1. However, the refinement of the structure was better in the latter spacegroup based on a 1.9% reduction in free R-factor at 2.54 for the same starting model when applying strong non-crystallographic symmetry (NCS) restraints (and with the reflections in the free set chosen in thin shells to avoid possible symmetry bias). The value of the free R-factor increased if NCS restraints were weakened, suggesting at most minimal conformational differences between protomers. However, the refined orientation of the NCS operator is inclined 0.04 degrees from the unit cell axis. This deviation from exact P2(1) symmetry is likely to account for the improved refinement statistics obtained in spacegroup P1, while its small size is consistent with the good merging statistics observed in spacegroup P2(1).
RfactorNum. reflection% reflectionSelection details
Rfree0.279 2036 10.2 %RANDOM
Rwork0.233 ---
all0.234 21841 --
obs0.233 19876 91 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.2457 Å2 / ksol: 0.45 e/Å3
Displacement parametersBiso mean: 27.9 Å2
Baniso -1Baniso -2Baniso -3
1-19.8 Å22.68 Å21.06 Å2
2---8.09 Å2-3.94 Å2
3----11.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.54→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5208 0 12 169 5389
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d0.92
LS refinement shellResolution: 2.54→2.63 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.369 153 9.3 %
Rwork0.276 1495 -
obs-1486 76.3 %

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