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- PDB-5x3n: Crystal structure of DiUb-K6 -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5x3n
TitleCrystal structure of DiUb-K6
ComponentsPolyubiquitin-B
KeywordsPROTEIN BINDING / Ubiquitin / Synthesis / phosphorylation
Function / homology
Function and homology information


symbiont entry into host cell via disruption of host cell glycocalyx / symbiont entry into host cell via disruption of host cell envelope / virus tail
Similarity search - Function
Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Pectin lyase fold / Pectin lyase fold/virulence factor / Ubiquitin family
Similarity search - Domain/homology
PHOSPHATE ION / Tail fiber
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.649 Å
AuthorsMan, P. / Shuai, G. / Qian, Q. / Lei, L.
CitationJournal: To Be Published
Title: Structure of p-Ub-S65-NH2 at 1.82 Angstroms resolution.
Authors: Man, P. / Shuai, G. / Qian, Q. / Lei, L.
History
DepositionFeb 6, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8624
Polymers8,5771
Non-polymers2853
Water1,20767
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area500 Å2
ΔGint-15 kcal/mol
Surface area4690 Å2
Unit cell
Length a, b, c (Å)26.048, 26.278, 46.193
Angle α, β, γ (deg.)102.05, 94.14, 99.63
Int Tables number2
Space group name H-MP-1

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Components

#1: Protein Polyubiquitin-B


Mass: 8576.831 Da / Num. of mol.: 1 / Fragment: UNP residues 1-76
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: P0CG47
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 1.77 Å3/Da / Density % sol: 30.36 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2M Magnesium formate dihydrate, 20%(w/v) Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jan 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.649→44.896 Å / Num. obs: 11102 / % possible obs: 78.55 % / Redundancy: 3.3 % / Net I/σ(I): 2.35

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.649→44.896 Å / SU ML: 0.13 / Cross valid method: NONE / σ(F): 1.33 / Phase error: 25.34
RfactorNum. reflection% reflection
Rfree0.2759 555 5 %
Rwork0.2158 --
obs0.219 11102 78.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.649→44.896 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms601 0 15 67 683
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006627
X-RAY DIFFRACTIONf_angle_d0.832845
X-RAY DIFFRACTIONf_dihedral_angle_d10.333387
X-RAY DIFFRACTIONf_chiral_restr0.05398
X-RAY DIFFRACTIONf_plane_restr0.006107
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6493-1.81530.283640.25941180X-RAY DIFFRACTION35
1.8153-2.0780.34131460.22652990X-RAY DIFFRACTION88
2.078-2.6180.30691540.22893161X-RAY DIFFRACTION94
2.618-44.91220.25231910.20553216X-RAY DIFFRACTION97

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