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- PDB-4p22: Crystal Structure of N-terminal Fragments of E1 -

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Basic information

Entry
Database: PDB / ID: 4p22
TitleCrystal Structure of N-terminal Fragments of E1
ComponentsUbiquitin-like modifier-activating enzyme 1
KeywordsLIGASE / E1 / ubiquitin
Function / homology
Function and homology information


E1 ubiquitin-activating enzyme / ubiquitin activating enzyme activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / protein ubiquitination / DNA damage response / mitochondrion / RNA binding / extracellular exosome ...E1 ubiquitin-activating enzyme / ubiquitin activating enzyme activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / protein ubiquitination / DNA damage response / mitochondrion / RNA binding / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ubiquitin-activating enzyme E1, FCCH domain / Ubiquitin-activating enzyme E1, conserved site / Ubiquitin-activating enzyme signature 1. / Ubiquitin-activating enzyme E1 / Ubiquitin-activating enzyme E1, C-terminal / Ubiquitin-activating enzyme E1, FCCH domain / Ubiquitin-activating enzyme E1, four-helix bundle / Ubiquitin-activating enzyme E1, C-terminal domain superfamily / Ubiquitin-activating enzyme E1, SCCH domain / Ubiquitin-activating enzyme E1, FCCH domain superfamily ...Ubiquitin-activating enzyme E1, FCCH domain / Ubiquitin-activating enzyme E1, conserved site / Ubiquitin-activating enzyme signature 1. / Ubiquitin-activating enzyme E1 / Ubiquitin-activating enzyme E1, C-terminal / Ubiquitin-activating enzyme E1, FCCH domain / Ubiquitin-activating enzyme E1, four-helix bundle / Ubiquitin-activating enzyme E1, C-terminal domain superfamily / Ubiquitin-activating enzyme E1, SCCH domain / Ubiquitin-activating enzyme E1, FCCH domain superfamily / Ubiquitin fold domain / Ubiquitin-activating enzyme E1 FCCH domain / Ubiquitin-activating enzyme E1 four-helix bundle / Ubiquitin-activating enzyme e1 C-terminal domain / Ubiquitin-activating enzyme, SCCH domain / Ubiquitin-activating enzyme, SCCH domain / Ubiquitin/SUMO-activating enzyme E1-like / Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1 / Ubiquitin-activating enzyme E1, Cys active site / Ubiquitin-activating enzyme active site. / ThiF/MoeB/HesA family / Ubiquitin-activating enzyme / THIF-type NAD/FAD binding fold / ThiF family / Elongation Factor Tu (Ef-tu); domain 3 / NAD(P)-binding Rossmann-like Domain / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-like modifier-activating enzyme 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.75 Å
AuthorsXie, S.-T.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31070643 China
National Natural Science Foundation of China (NSFC)31130062 China
CitationJournal: Biosci.Biotechnol.Biochem. / Year: 2014
Title: Expression, purification, and crystal structure of N-terminal domains of human ubiquitin-activating enzyme (E1).
Authors: Xie, S.T.
History
DepositionFeb 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)96,9162
Polymers96,9162
Non-polymers00
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-26 kcal/mol
Surface area29680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.126, 186.812, 135.222
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-508-

HOH

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Components

#1: Protein Ubiquitin-like modifier-activating enzyme 1 / Protein A1S9 / Ubiquitin-activating enzyme E1


Mass: 48457.922 Da / Num. of mol.: 2 / Fragment: UNP residues 1-439 / Mutation: G197D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBA1, A1S9T, UBE1 / Plasmid: pET-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P22314
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 3.07 Å3/Da / Density % sol: 59.89 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Na3Citrate pH 5.6, 3.0 M NH4Ac

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.975 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 2.748→50 Å / Num. obs: 30860 / % possible obs: 98.4 % / Redundancy: 7.7 % / Biso Wilson estimate: 38.11 Å2 / Net I/σ(I): 11.3

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data collection
PDB_EXTRACT3.14data extraction
RefinementResolution: 2.75→29.77 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.264 1559 5.05 %
Rwork0.205 --
obs0.208 30860 98.3 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.09 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 46.77 Å2
Baniso -1Baniso -2Baniso -3
1--3.016 Å20 Å20 Å2
2--10.3126 Å20 Å2
3----7.9316 Å2
Refinement stepCycle: final / Resolution: 2.75→29.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5739 0 0 109 5848
Biso mean---33.77 -
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015847
X-RAY DIFFRACTIONf_angle_d1.377915
X-RAY DIFFRACTIONf_dihedral_angle_d17.7432139
X-RAY DIFFRACTIONf_chiral_restr0.09894
X-RAY DIFFRACTIONf_plane_restr0.0051040
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.83650.2972990.26312283X-RAY DIFFRACTION85
2.8365-2.93780.38031370.27072568X-RAY DIFFRACTION96
2.9378-3.05530.3371410.26492687X-RAY DIFFRACTION100
3.0553-3.19420.3271420.23922674X-RAY DIFFRACTION100
3.1942-3.36240.28121540.22212689X-RAY DIFFRACTION100
3.3624-3.57270.27611450.21072679X-RAY DIFFRACTION100
3.5727-3.84810.25551540.19652676X-RAY DIFFRACTION100
3.8481-4.23430.24161500.17452720X-RAY DIFFRACTION100
4.2343-4.84480.22471590.16352703X-RAY DIFFRACTION100
4.8448-6.09530.28221350.21222769X-RAY DIFFRACTION100
6.0953-29.76690.20291430.18392853X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -33.4667 Å / Origin y: 29.682 Å / Origin z: 8.5139 Å
111213212223313233
T0.0098 Å20.0031 Å20.0096 Å2-0.0133 Å20.0368 Å2---0.0068 Å2
L0.8398 °20.2938 °2-0.0434 °2-0.31 °20.2467 °2--0.7546 °2
S-0.098 Å °0.0683 Å °-0.1409 Å °0.0486 Å °-0.0053 Å °-0.0903 Å °0.1709 Å °0.0902 Å °0.03 Å °
Refinement TLS groupSelection details: ALL

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