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- PDB-4gu2: Crystal structure of ubiquitin from Entamoeba histolytica to 1.35... -

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Basic information

Entry
Database: PDB / ID: 4gu2
TitleCrystal structure of ubiquitin from Entamoeba histolytica to 1.35 Angstrom
ComponentsUbiquitin
KeywordsPROTEIN BINDING / ubiquitin / ubiquitin-like modifier / ubiquitin fold / post-translational ubiquitination / isopeptide bond / EhUbc5 / EhUba1
Function / homology
Function and homology information


modification-dependent protein catabolic process / protein tag activity / protein ubiquitination / ubiquitin protein ligase binding / nucleus / cytoplasm
Similarity search - Function
Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain ...Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsBosch, D.E. / Siderovski, D.P.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural Determinants of Ubiquitin Conjugation in Entamoeba histolytica.
Authors: Bosch, D.E. / Siderovski, D.P.
History
DepositionAug 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2012Group: Database references
Revision 1.2Feb 13, 2013Group: Database references
Revision 1.3Sep 13, 2023Group: 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)8,9821
Polymers8,9821
Non-polymers00
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.798, 49.798, 63.830
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-134-

HOH

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Components

#1: Protein Ubiquitin / Ubiquitin / putative


Mass: 8982.275 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote)
Gene: EhUBI1, EHI_083270, EHI_083410, EHI_156660, EHI_178340
Plasmid: pLIC His / Production host: Escherichia coli (E. coli) / References: UniProt: C4M760
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.54 Å3/Da / Density % sol: 51.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: EhUbiquitin at 17 mg/mL was mixed 1:1 with and equilibrated against crystallization solution containing 25% (w/v) PEG 3350 and 100 mM citric acid, pH 3.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 8, 2012
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→25.654 Å / Num. all: 20637 / Num. obs: 20493 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19.2 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 100
Reflection shellResolution: 1.35→1.36 Å / Redundancy: 17.9 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 6.9 / Num. unique all: 486 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXAutoMRmodel building
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXAutoMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1UBQ

1ubq


Resolution: 1.35→25.65 Å / SU ML: 0.14 / σ(F): 1.38 / Phase error: 30.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2692 1028 5.03 %RANDOM
Rwork0.212 ---
obs0.215 20454 99.03 %-
all-20654 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.35→25.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms546 0 0 66 612
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015574
X-RAY DIFFRACTIONf_angle_d1.642770
X-RAY DIFFRACTIONf_dihedral_angle_d14.6230
X-RAY DIFFRACTIONf_chiral_restr0.07989
X-RAY DIFFRACTIONf_plane_restr0.009100
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.35-1.42050.31251430.22822718271898
1.4205-1.50950.30261470.21232752100
1.5095-1.62610.27831450.2062757100
1.6261-1.78970.2711450.21632773100
1.7897-2.04860.26921450.20442787100
2.0486-2.58060.23751490.22432826100
2.5806-25.65880.27711540.2078281396

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