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- PDB-5ia8: Structure of a Ubiquitin like protein with an E1 fragment -

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Basic information

Entry
Database: PDB / ID: 5ia8
TitleStructure of a Ubiquitin like protein with an E1 fragment
ComponentsUbiquitin-like modifier-activating enzyme 5,Ubiquitin-fold modifier 1
KeywordsCELL CYCLE / Ubiquitin like protein
Function / homology
Function and homology information


UFM1 activating enzyme activity / ubiquitin-like modifier activating enzyme activity / protein K69-linked ufmylation / protein ufmylation / megakaryocyte differentiation / regulation of type II interferon production / regulation of intracellular estrogen receptor signaling pathway / reticulophagy / neuromuscular process / negative regulation of protein import into nucleus ...UFM1 activating enzyme activity / ubiquitin-like modifier activating enzyme activity / protein K69-linked ufmylation / protein ufmylation / megakaryocyte differentiation / regulation of type II interferon production / regulation of intracellular estrogen receptor signaling pathway / reticulophagy / neuromuscular process / negative regulation of protein import into nucleus / response to endoplasmic reticulum stress / erythrocyte differentiation / brain development / Antigen processing: Ubiquitination & Proteasome degradation / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / negative regulation of apoptotic process / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / zinc ion binding / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ubiquitin-fold modifier 1 / Ubiquitin fold modifier 1 protein / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / ThiF/MoeB/HesA family / THIF-type NAD/FAD binding fold / ThiF family / Ubiquitin-activating enzyme / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) ...Ubiquitin-fold modifier 1 / Ubiquitin fold modifier 1 protein / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / ThiF/MoeB/HesA family / THIF-type NAD/FAD binding fold / ThiF family / Ubiquitin-activating enzyme / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-like modifier-activating enzyme 5 / Ubiquitin-fold modifier 1 / Ubiquitin-like modifier-activating enzyme 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsOweis, W. / Padala, P. / Wiener, R.
Funding support Israel, 1items
OrganizationGrant numberCountry
BSF Israel
CitationJournal: Sci Rep / Year: 2017
Title: Novel insights into the interaction of UBA5 with UFM1 via a UFM1-interacting sequence.
Authors: Padala, P. / Oweis, W. / Mashahreh, B. / Soudah, N. / Cohen-Kfir, E. / Todd, E.A. / Berndsen, C.E. / Wiener, R.
History
DepositionFeb 21, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin-like modifier-activating enzyme 5,Ubiquitin-fold modifier 1
B: Ubiquitin-like modifier-activating enzyme 5,Ubiquitin-fold modifier 1


Theoretical massNumber of molelcules
Total (without water)21,1502
Polymers21,1502
Non-polymers00
Water91951
1
A: Ubiquitin-like modifier-activating enzyme 5,Ubiquitin-fold modifier 1


Theoretical massNumber of molelcules
Total (without water)10,5751
Polymers10,5751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ubiquitin-like modifier-activating enzyme 5,Ubiquitin-fold modifier 1


Theoretical massNumber of molelcules
Total (without water)10,5751
Polymers10,5751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.940, 46.940, 201.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: _ / Auth seq-ID: -11 - 77 / Label seq-ID: 3 - 91

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Ubiquitin-like modifier-activating enzyme 5,Ubiquitin-fold modifier 1


Mass: 10575.112 Da / Num. of mol.: 2 / Fragment: UNP residues 334-346,UNP residues 1-83
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBA5, UFM1, C13orf20, BM-002 / Production host: Escherichia coli (E. coli)
References: UniProt: E7EQ61, UniProt: P61960, UniProt: Q9GZZ9*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.62 Å3/Da / Density % sol: 53.06 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.2M Potassium phosphate dibasic and 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 2→50.3 Å / Num. obs: 16255 / % possible obs: 100 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.096
Reflection shellHighest resolution: 2 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5iaa

5iaa


Resolution: 2→50.3 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.941 / SU B: 9.074 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.148 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23627 854 5.3 %RANDOM
Rwork0.22133 ---
obs0.22212 15330 99.99 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.6 Å
Displacement parametersBiso mean: 41.956 Å2
Baniso -1Baniso -2Baniso -3
1-1.67 Å2-0 Å2-0 Å2
2--1.67 Å2-0 Å2
3----3.34 Å2
Refinement stepCycle: 1 / Resolution: 2→50.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1394 0 0 51 1445
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191426
X-RAY DIFFRACTIONr_bond_other_d0.0050.021401
X-RAY DIFFRACTIONr_angle_refined_deg1.4491.9721943
X-RAY DIFFRACTIONr_angle_other_deg1.2233245
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1895180
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.7132552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.00215239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.768154
X-RAY DIFFRACTIONr_chiral_restr0.0890.2233
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211564
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02288
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3372.329726
X-RAY DIFFRACTIONr_mcbond_other2.3382.33725
X-RAY DIFFRACTIONr_mcangle_it3.5553.479904
X-RAY DIFFRACTIONr_mcangle_other3.5533.479905
X-RAY DIFFRACTIONr_scbond_it3.2852.698700
X-RAY DIFFRACTIONr_scbond_other3.2832.698701
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0873.8881040
X-RAY DIFFRACTIONr_long_range_B_refined6.74918.4991490
X-RAY DIFFRACTIONr_long_range_B_other6.74218.3341478
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 9480 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 67 -
Rwork0.284 1106 -
obs--99.91 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.71780.2897-0.03481.08650.5316.1370.129-0.05650.1350.02640.0169-0.0151-0.29390.2595-0.14590.0513-0.00670.06030.02790.00140.088316.1136.1887.924
25.23230.2721-0.74190.6042-0.45533.5140.21570.1291-0.5971-0.1067-0.11360.11360.3916-0.007-0.1020.11860.0321-0.03740.0318-0.03520.1571-0.378-7.23710.559
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-13 - 78
2X-RAY DIFFRACTION2B-11 - 78

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