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- PDB-6fj7: Caldiarchaeum Subterraneum Ubiquitin -

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Basic information

Entry
Database: PDB / ID: 6fj7
TitleCaldiarchaeum Subterraneum Ubiquitin
ComponentsUbiquitin-like protein
KeywordsPROTEIN BINDING / ubiquitination / ubiquitylation
Function / homology
Function and homology information


polyubiquitin modification-dependent protein binding / ubiquitin-dependent protein catabolic process / metal ion binding / cytosol
Similarity search - Function
: / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-like protein
Similarity search - Component
Biological speciesCandidatus Caldiarchaeum subterraneum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsWojtynek, M. / Martin, J. / Hartmann, M.D.
CitationJournal: Nat Commun / Year: 2018
Title: Rpn11-mediated ubiquitin processing in an ancestral archaeal ubiquitination system.
Authors: Fuchs, A.C.D. / Maldoner, L. / Wojtynek, M. / Hartmann, M.D. / Martin, J.
History
DepositionJan 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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: Ubiquitin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,5523
Polymers8,3601
Non-polymers1922
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-16 kcal/mol
Surface area4880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.450, 42.800, 51.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ubiquitin-like protein


Mass: 8359.806 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Caldiarchaeum subterraneum (archaea)
Gene: CSUB_C1474, HGMM_F04B03C03, HGMM_F21D07C21, HGMM_F30C12C33
Production host: Escherichia coli (E. coli) / References: UniProt: E6N8B8
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 1.94 Å3/Da / Density % sol: 36.53 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 100 mM sodium acetate pH 4.5, 200 mM lithium sulfate, 50% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.05→32.9 Å / Num. obs: 30589 / % possible obs: 98.2 % / Redundancy: 11 % / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Net I/σ(I): 22.39
Reflection shellResolution: 1.05→1.11 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.627 / Mean I/σ(I) obs: 2.18 / Num. unique obs: 4406 / CC1/2: 0.862 / % possible all: 89

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UBQ

1ubq


Resolution: 1.05→32.89 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.946 / SU B: 0.938 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.034 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19512 1530 5 %RANDOM
Rwork0.1534 ---
obs0.15544 29058 98.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0 Å20 Å2
2---0.37 Å20 Å2
3---0.34 Å2
Refinement stepCycle: 1 / Resolution: 1.05→32.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms569 0 10 76 655
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.019700
X-RAY DIFFRACTIONr_bond_other_d0.0020.02740
X-RAY DIFFRACTIONr_angle_refined_deg2.3372.047978
X-RAY DIFFRACTIONr_angle_other_deg0.90731728
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6895107
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.23822.77818
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.56115133
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.89155
X-RAY DIFFRACTIONr_chiral_restr0.130.2124
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021789
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02126
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6271.304362
X-RAY DIFFRACTIONr_mcbond_other1.5711.299360
X-RAY DIFFRACTIONr_mcangle_it2.0061.97460
X-RAY DIFFRACTIONr_mcangle_other2.021.974461
X-RAY DIFFRACTIONr_scbond_it2.631.568338
X-RAY DIFFRACTIONr_scbond_other2.6121.553330
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.962.215490
X-RAY DIFFRACTIONr_long_range_B_refined3.46511.525780
X-RAY DIFFRACTIONr_long_range_B_other3.36810.988753
X-RAY DIFFRACTIONr_rigid_bond_restr4.48931440
X-RAY DIFFRACTIONr_sphericity_free29.21514
X-RAY DIFFRACTIONr_sphericity_bonded10.0251478
LS refinement shellResolution: 1.049→1.076 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 94 -
Rwork0.32 1791 -
obs--83.04 %

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