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- PDB-5x3o: Crystal structure of p-DiUb-S65-COOH -

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Basic information

Entry
Database: PDB / ID: 5x3o
TitleCrystal structure of p-DiUb-S65-COOH
Components
  • D-ubiquitin
  • Polyubiquitin-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
polypeptide(D) / polypeptide(D) (> 10) / Tail fiber
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.194 Å
AuthorsMan, P. / Shuai, G. / Qian, Q. / Lei, L.
CitationJournal: To Be Published
Title: Structure of p-DiUb-S65-COOH at 2.19 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 1.1Feb 9, 2022Group: Database references / Category: database_2
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
D: D-ubiquitin


Theoretical massNumber of molelcules
Total (without water)17,2512
Polymers17,2512
Non-polymers00
Water1,09961
1
A: Polyubiquitin-B

D: D-ubiquitin


Theoretical massNumber of molelcules
Total (without water)17,2512
Polymers17,2512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area1320 Å2
ΔGint-11 kcal/mol
Surface area7740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.608, 33.764, 44.686
Angle α, β, γ (deg.)90.00, 103.49, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: Protein Polyubiquitin-B


Mass: 8656.811 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: Protein D-ubiquitin


Mass: 8593.780 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 1.75 Å3/Da / Density % sol: 29.89 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2M Ammonium phosphate monobasic, 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: Dec 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.194→43.453 Å / Num. obs: 6127 / % possible obs: 98.54 % / Redundancy: 6.1 % / Net I/σ(I): 2.53

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.194→43.453 Å / SU ML: 0.33 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 42.3 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.3153 315 5.14 %
Rwork0.2403 --
obs0.2445 6127 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.194→43.453 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1186 0 0 61 1247
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081208
X-RAY DIFFRACTIONf_angle_d1.0891631
X-RAY DIFFRACTIONf_dihedral_angle_d11.841781
X-RAY DIFFRACTIONf_chiral_restr0.063195
X-RAY DIFFRACTIONf_plane_restr0.007209
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1936-2.76360.40271640.26062884X-RAY DIFFRACTION99
2.7636-43.46130.28561510.23292928X-RAY DIFFRACTION98

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