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- PDB-1aar: STRUCTURE OF A DIUBIQUITIN CONJUGATE AND A MODEL FOR INTERACTION ... -

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Basic information

Entry
Database: PDB / ID: 1aar
TitleSTRUCTURE OF A DIUBIQUITIN CONJUGATE AND A MODEL FOR INTERACTION WITH UBIQUITIN CONJUGATING ENZYME (E2)
ComponentsDI-UBIQUITIN
KeywordsUBIQUITIN
Function / homologyUbiquitin domain / Ubiquitin conserved site / Ubiquitin / Ubiquitin-like domain superfamily / Ubiquitin family / Ubiquitin domain signature. / Ubiquitin domain profile. / nucleus / cytoplasm / Polyubiquitin-C / Polyubiquitin-C
Function and homology information
Specimen sourceBos taurus (cattle)
MethodX-RAY DIFFRACTION / 2.3 Å resolution
AuthorsCook, W.J. / Jeffrey, L.C. / Carson, M. / Chen, Z. / Pickart, C.M.
CitationJournal: J.Biol.Chem. / Year: 1992
Title: Structure of a diubiquitin conjugate and a model for interaction with ubiquitin conjugating enzyme (E2).
Authors: Cook, W.J. / Jeffrey, L.C. / Carson, M. / Chen, Z. / Pickart, C.M.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 17, 1992 / Release: Oct 31, 1993
RevisionDateData content typeGroupProviderType
1.0Oct 31, 1993Structure modelrepositoryInitial release
1.1Mar 10, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DI-UBIQUITIN
B: DI-UBIQUITIN


Theoretical massNumber of molelcules
Total (without water)17,1542
Polyers17,1542
Non-polymers00
Water27015
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)1480
ΔGint (kcal/M)-8
Surface area (Å2)7950
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)32.100, 46.200, 25.400
Angle α, β, γ (deg.)105.90, 113.30, 69.70
Int Tables number1
Space group name H-MP 1
Atom site foot note1: THERE IS AN UNUSUAL ISOPEPTIDE BOND BETWEEN THE SIDE CHAIN OF LYS B 48 FROM ONE UBIQUITIN MOIETY AND THE CARBOXYL TERMINUS GLY A 76 OF THE OTHER UBIQUITIN MOIETY.

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Components

#1: Protein/peptide DI-UBIQUITIN


Mass: 8576.831 Da / Num. of mol.: 2 / Source: (gene. exp.) Bos taurus (cattle) / Genus: Bos / References: UniProt: P62990, UniProt: P0CH28*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Formula: H2O / Water
Compound detailsTHERE IS AN UNUSUAL ISOPEPTIDE BOND BETWEEN THE SIDE CHAIN OF LYS B 48 FROM ONE UBIQUITIN MOIETY ...THERE IS AN UNUSUAL ISOPEPTIDE BOND BETWEEN THE SIDE CHAIN OF LYS B 48 FROM ONE UBIQUITIN MOIETY AND THE CARBOXYL TERMINUS GLY A 76 OF THE OTHER UBIQUITIN MOIETY.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.87 / Density percent sol: 34.12 %
Crystal grow
*PLUS
Temp: 4 ℃ / Method: other / Details: using macroseeding / PH range low: 4.6 / PH range high: 4
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol ID
136-42 %MPD11
20.05 Msodium citrate11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
D resolution high: 2.3 Å / Number obs: 5392 / Number measured all: 17483 / Rmerge I obs: 0.066

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
Least-squares processR factor R work: 0.19 / R factor obs: 0.19 / Highest resolution: 2.3 Å
Refine hist #LASTHighest resolution: 2.3 Å
Number of atoms included #LASTProtein: 1203 / Nucleic acid: 0 / Ligand: 0 / Solvent: 15 / Total: 1218
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.020
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg4.0
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine
*PLUS
Sigma F: 2
Least-squares process
*PLUS
R factor obs: 0.19 / Highest resolution: 2.3 Å / Lowest resolution: 6 Å / Number reflection all: 5085 / Number reflection obs: 5074
Refine LS restraints
*PLUS
Type: x_angle_d
Refine LS shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.41 Å / Number reflection obs: 652 / R factor obs: 0.196 / Total number of bins used: 7

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