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- PDB-5xpk: Crystal structure of ubiquitin-k6mimic -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5xpk
TitleCrystal structure of ubiquitin-k6mimic
Components
  • D-ubiquitin
  • Ubiquitin
KeywordsPROTEIN BINDING / Ubiquitin / Synthesis
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 / Resolution: 2.274 Å
AuthorsMan, P. / Shuai, G. / Qian, Q. / Lei, L.
CitationJournal: To Be Published
Title: Structure of ubiquitin-k6mimic at 2.27 Angstroms resolution.
Authors: Man, P. / Shuai, G. / Qian, Q. / Lei, L.
History
DepositionJun 3, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Ubiquitin
B: D-ubiquitin


Theoretical massNumber of molelcules
Total (without water)17,1642
Polymers17,1642
Non-polymers00
Water27015
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)26.656, 46.626, 40.495
Angle α, β, γ (deg.)90.00, 91.47, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-76-

GLY

21B-101-

HOH

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Components

#1: Protein Ubiquitin


Mass: 8593.862 Da / Num. of mol.: 1
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: 8569.782 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P0CG47*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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

Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2M Ammonium formate, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Oct 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.274→40.482 Å / Num. obs: 4160 / % possible obs: 97.3 % / Redundancy: 2.9 % / Net I/σ(I): 9.39
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.16 / % possible all: 80

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Processing

SoftwareName: PHENIX / Version: (1.10.1_2155) / Classification: refinement
RefinementResolution: 2.274→40.482 Å / SU ML: 0.45 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 29.39
RfactorNum. reflection% reflection
Rfree0.3103 243 5.84 %
Rwork0.2501 --
obs0.2543 4160 89.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.274→40.482 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1202 0 0 15 1217
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031213
X-RAY DIFFRACTIONf_angle_d0.6631631
X-RAY DIFFRACTIONf_dihedral_angle_d20.815618
X-RAY DIFFRACTIONf_chiral_restr0.051194
X-RAY DIFFRACTIONf_plane_restr0.004210
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.274-2.86490.39481070.29161710X-RAY DIFFRACTION79
2.8649-40.48810.28231360.23632207X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2718-0.0513-0.02780.01180.0050.00090.097-0.1720.0421-0.1354-0.50890.4945-0.0086-0.4209-0.00490.3865-0.011-0.04530.34750.01280.4135-2.0593-2.00326.3238
20.08340.0431-0.13380.0577-0.12690.3135-0.0767-0.0587-0.0057-0.03280.0983-0.20660.18650.14710.07410.72010.6746-0.09390.493-1.09481.12557.127-11.90451.3454
30.40670.44290.37240.77740.2940.36490.2338-0.341-0.10990.273-0.16460.3620.6057-0.50390.05260.2098-0.051-0.0470.25530.14020.3224-1.1722-0.525912.913
40.0726-0.0490.00490.0478-0.04740.05720.0022-0.1528-0.29250.57620.454-0.38990.57270.03290.00050.40410.01360.00130.34040.0070.34954.0499-7.121815.5693
50.0214-0.0655-0.01240.18530.04050.0161-0.3305-0.27720.3525-0.03790.0845-0.93240.35660.66270.00290.36790.1249-0.04270.5752-0.01130.368711.6673-8.412813.1047
60.33740.18970.58810.58650.01521.76820.0670.36830.2508-0.13340.0285-0.62010.620.68450.01890.359-0.0875-0.00130.24970.04160.398710.06914.777311.0961
70.01660.0028-0.02860.0039-0.00150.03370.27880.23730.2624-0.4507-0.5282-0.1645-0.2644-0.2607-0.00020.31660.07970.04340.30920.08590.443-0.83655.21363.8774
80.03150.0089-0.02230.03860.05010.0809-0.01340.6380.1528-0.1826-0.1297-0.16220.05590.28340.00010.41270.0194-0.04040.37240.02820.29758.1141-4.84864.8748
90.8096-1.033-0.24861.3190.31780.0774-0.07450.03540.07150.1391-0.07780.2-0.21090.0676-0.01990.716-0.33360.05110.886-0.00660.690820.4404-8.770314.1634
100.4381-0.2262-0.27220.61180.00250.8238-0.05880.0753-0.0267-0.41910.0692-0.1550.1732-0.0208-0.00030.26870.0330.01530.26550.01980.2545-7.3965-26.61429.1837
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 5 )
2X-RAY DIFFRACTION2chain 'A' and (resid 7 through 12 )
3X-RAY DIFFRACTION3chain 'A' and (resid 13 through 22 )
4X-RAY DIFFRACTION4chain 'A' and (resid 23 through 34 )
5X-RAY DIFFRACTION5chain 'A' and (resid 35 through 44 )
6X-RAY DIFFRACTION6chain 'A' and (resid 45 through 59 )
7X-RAY DIFFRACTION7chain 'A' and (resid 60 through 64 )
8X-RAY DIFFRACTION8chain 'A' and (resid 65 through 71 )
9X-RAY DIFFRACTION9chain 'A' and (resid 72 through 76 )
10X-RAY DIFFRACTION10chain 'B' and (resid 10 through 76 )

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