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- PDB-5vix: Crystal structure of Polyubiquitin with 3 ub domains, domains 1 a... -

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Basic information

Entry
Database: PDB / ID: 5vix
TitleCrystal structure of Polyubiquitin with 3 ub domains, domains 1 and 2, from Naegleria fowleri ATCC 30863
ComponentsPolyubiquitin
KeywordsUNKNOWN FUNCTION / SSGCID / Structural Genomics / Naegleria fowleri / polyubiquitin / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
NITRATE ION / Polyubiquitin
Similarity search - Component
Biological speciesNaegleria fowleri (brain-eating amoeba)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of polyubiquitin with 3 ub domains, domains 1 and 2, from Naegleria fowleri ATCC 30863
Authors: Abendroth, J. / Mayclin, S.J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionApr 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.2Jul 3, 2019Group: Data collection / Database references / Structure summary
Category: citation / struct / Item: _citation.title / _struct.title
Revision 2.0Jun 17, 2020Group: Atomic model / Data collection / Source and taxonomy / Category: atom_site / entity_src_gen / pdbx_nonpoly_scheme
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_nonpoly_scheme.auth_seq_num
Revision 2.1Oct 4, 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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4194
Polymers18,2331
Non-polymers1863
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.020, 67.710, 35.830
Angle α, β, γ (deg.)90.000, 114.490, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Polyubiquitin


Mass: 18232.789 Da / Num. of mol.: 1 / Fragment: UNP residues 1-152
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Naegleria fowleri (brain-eating amoeba)
Plasmid: NafoA.19251.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D2V6G7
#2: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.05 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Rigaku Reagents JCSG+ C3: 200mM Ammonium nitrate, 20% PEG 3350: NafoA.19251.a.B1.PS38167 at 20mg/ml: cryo: 20% EG: tray 288541C3: puck FIQ0-2.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 12, 2016
RadiationMonochromator: Diamond[111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.55→32.608 Å / Num. obs: 21353 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 4.16 % / Biso Wilson estimate: 19.21 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.061 / Χ2: 1.06 / Net I/σ(I): 14
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.55-1.594.0560.5672.3115490.8730.65399.7
1.59-1.634.2320.4622.8815570.9330.52798
1.63-1.684.1780.3743.4714600.9560.42899.4
1.68-1.734.230.2944.514370.9660.33698.8
1.73-1.794.20.2225.9414280.980.25398.6
1.79-1.854.2020.177.4213290.9880.19599.8
1.85-1.924.2080.12610.0113280.9910.14499
1.92-24.1860.10212.2912790.9930.11698.4
2-2.094.2050.08614.8712030.9940.098100
2.09-2.194.1870.07117.0911560.9960.08199
2.19-2.314.1290.05919.4110980.9960.06899.5
2.31-2.454.1650.05621.0710600.9960.06499.3
2.45-2.624.1260.05222.739830.9960.0699.5
2.62-2.834.130.04824.899280.9960.05599.6
2.83-3.14.1090.04427.048440.9970.0599.3
3.1-3.474.1050.04229.157700.9960.04899.5
3.47-44.0940.03930.656700.9980.04599.4
4-4.94.0970.03631.315800.9970.04198.8
4.9-6.934.0850.03630.664470.9980.04199.1
6.93-503.8420.03730.462470.9950.04496.9

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
ARPmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5h07

5h07


Resolution: 1.55→32.608 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.68
RfactorNum. reflection% reflectionSelection details
Rfree0.2041 1862 8.73 %RANDOM SELECTION, 0
Rwork0.1709 ---
obs0.1739 21330 99.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.72 Å2 / Biso mean: 31.2474 Å2 / Biso min: 12.62 Å2
Refinement stepCycle: final / Resolution: 1.55→32.608 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1214 0 12 170 1396
Biso mean--34.73 40.39 -
Num. residues----154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071315
X-RAY DIFFRACTIONf_angle_d0.9371792
X-RAY DIFFRACTIONf_chiral_restr0.061215
X-RAY DIFFRACTIONf_plane_restr0.005236
X-RAY DIFFRACTIONf_dihedral_angle_d14.691830
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5501-1.5920.32191520.257814571609100
1.592-1.63880.2761390.25121497163698
1.6388-1.69170.31491480.24451482163099
1.6917-1.75220.26381390.22341460159999
1.7522-1.82230.25811520.20781496164899
1.8223-1.90530.21971470.18651490163799
1.9053-2.00570.19751270.17221519164699
2.0057-2.13140.22251140.164515241638100
2.1314-2.29590.2071390.17515091648100
2.2959-2.52680.2261190.180415341653100
2.5268-2.89230.211500.180514961646100
2.8923-3.64320.19051700.15614841654100
3.6432-32.61470.16651660.1411520168699
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)
13.2426-4.6505-4.03447.83155.81669.8852-0.1342-0.1770.00620.28180.2426-0.32850.89860.3525-0.21030.25030.0388-0.00190.2510.01840.24647.5946-3.75916.4503
24.21360.20852.35761.2468-1.34763.19120.1382-0.4812-0.1070.31430.2244-0.05220.5995-0.3884-0.30230.2168-0.02660.00370.22380.08070.18340.9897-1.97898.6484
36.82640.6622-1.3878.0209-1.00734.36-0.0013-0.2792-0.642-0.0357-0.03640.53520.5759-0.5180.05490.1955-0.0739-0.04910.21890.04190.2393-6.3873-2.94913.2072
45.2705-0.40312.85575.4804-0.03724.1212-0.01690.2713-0.0685-0.2201-0.0611-0.12830.04240.22280.04470.1393-0.00660.01780.16640.01850.10514.9983.0432-1.0075
51.3035-1.32710.34521.8607-0.53160.1395-0.3218-0.5122-0.11970.04640.26010.43810.2414-0.9406-0.00610.1304-0.0621-0.01060.45340.00610.2434-9.06776.94383.2739
62.12061.31723.07636.6430.32255.4244-0.0832-0.166-0.19040.50150.0977-0.23990.57320.5671-0.00950.1888-0.0029-0.00930.39170.02210.1582-4.53986.0354-13.7432
76.19510.16983.46216.3094-0.3595.6534-0.1627-0.4470.55930.4557-0.1423-0.045-0.57860.07870.34640.2412-0.0432-0.00970.2119-0.07680.1588-6.220717.3089-11.4785
87.18032.29623.15685.10840.58581.4452-0.51410.74540.3862-0.32240.0462-0.4975-0.54231.50370.12690.1886-0.1735-0.01930.52530.06830.26010.509516.0274-19.4796
97.5050.07240.62416.98123.42946.181-0.0941-0.13330.4657-0.2172-0.18950.467-0.5574-0.35580.17230.13510.012-0.01810.2148-0.05530.1703-13.86214.871-19.9717
103.71213.5212-3.44847.3711-2.81173.486-0.47310.3755-0.3301-0.07210.2047-0.9129-0.1844-0.01310.08130.1955-0.02750.00840.3034-0.00070.2620.086310.7112-22.3244
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -3 through 7 )A-3 - 7
2X-RAY DIFFRACTION2chain 'A' and (resid 8 through 22 )A8 - 22
3X-RAY DIFFRACTION3chain 'A' and (resid 23 through 44 )A23 - 44
4X-RAY DIFFRACTION4chain 'A' and (resid 45 through 65 )A45 - 65
5X-RAY DIFFRACTION5chain 'A' and (resid 66 through 77 )A66 - 77
6X-RAY DIFFRACTION6chain 'A' and (resid 78 through 92 )A78 - 92
7X-RAY DIFFRACTION7chain 'A' and (resid 93 through 110 )A93 - 110
8X-RAY DIFFRACTION8chain 'A' and (resid 111 through 120 )A111 - 120
9X-RAY DIFFRACTION9chain 'A' and (resid 121 through 141 )A121 - 141
10X-RAY DIFFRACTION10chain 'A' and (resid 142 through 150 )A142 - 150

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