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- PDB-6fjv: Rpn11 homolog from Caldiarchaeum Subterraneum, truncated -

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Basic information

Entry
Database: PDB / ID: 6fjv
TitleRpn11 homolog from Caldiarchaeum Subterraneum, truncated
Components26S proteasome regulatory subunit N11-like protein
KeywordsHYDROLASE / deubiquitination / deubiquitylation
Function / homology
Function and homology information


proteasome complex / metallopeptidase activity / metal ion binding
Similarity search - Function
Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / : / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
26S proteasome regulatory subunit N11-like protein
Similarity search - Component
Biological speciesCandidatus Caldiarchaeum subterraneum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsFuchs, A.C.D. / Albrecht, R. / 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 23, 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

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Assembly

Deposited unit
A: 26S proteasome regulatory subunit N11-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2543
Polymers17,0621
Non-polymers1922
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-18 kcal/mol
Surface area8110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.954, 38.954, 194.018
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein 26S proteasome regulatory subunit N11-like protein


Mass: 17061.760 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Caldiarchaeum subterraneum (archaea)
Gene: CSUB_C1473, HGMM_F04B03C04, HGMM_F21D07C20, HGMM_F30C12C32
Production host: Escherichia coli (E. coli) / References: UniProt: E6N8B9
#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.: 139 / 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: 2.16 Å3/Da / Density % sol: 42.97 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 100 mM sodium acetate pH 4.6, 1.5 M ammonium sulfate, 25% PEG 4000

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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: Oct 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→38.2 Å / Num. obs: 34313 / % possible obs: 100 % / Redundancy: 12.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Net I/σ(I): 21.1
Reflection shellResolution: 1.35→1.43 Å / Redundancy: 11.5 % / Rmerge(I) obs: 1.11 / Mean I/σ(I) obs: 2.25 / CC1/2: 0.917 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FJU

6fju


Resolution: 1.35→38.2 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.01 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.059 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21047 1728 5 %RANDOM
Rwork0.17063 ---
obs0.17264 32583 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.995 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0 Å20 Å2
2---0.06 Å2-0 Å2
3---0.12 Å2
Refinement stepCycle: 1 / Resolution: 1.35→38.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1130 0 10 139 1279
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191238
X-RAY DIFFRACTIONr_bond_other_d0.0030.021223
X-RAY DIFFRACTIONr_angle_refined_deg1.7321.9791697
X-RAY DIFFRACTIONr_angle_other_deg0.8432823
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.255167
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.80523.26146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.00715218
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.731157
X-RAY DIFFRACTIONr_chiral_restr0.1060.2201
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211382
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02271
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_it2.2821.555615
X-RAY DIFFRACTIONr_mcbond_other2.2851.555614
X-RAY DIFFRACTIONr_mcangle_it2.6122.345772
X-RAY DIFFRACTIONr_mcangle_other2.6112.346773
X-RAY DIFFRACTIONr_scbond_it3.1811.983623
X-RAY DIFFRACTIONr_scbond_other3.031.931614
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5092.753903
X-RAY DIFFRACTIONr_long_range_B_refined4.43814.6211498
X-RAY DIFFRACTIONr_long_range_B_other3.83213.9411450
X-RAY DIFFRACTIONr_rigid_bond_restr3.77332461
X-RAY DIFFRACTIONr_sphericity_free27.187541
X-RAY DIFFRACTIONr_sphericity_bonded12.05952527
LS refinement shellResolution: 1.348→1.383 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 128 -
Rwork0.367 2344 -
obs--99.6 %

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