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- PDB-6fnn: Caldiarchaeum Subterraneum Ubiquitin:Rpn11-homolog complex -

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Basic information

Entry
Database: PDB / ID: 6fnn
TitleCaldiarchaeum Subterraneum Ubiquitin:Rpn11-homolog complex
Components
  • 26S proteasome regulatory subunit N11-like protein
  • Ubiquitin-like protein
KeywordsHYDROLASE / deubiquitination / deubiquitylation / JAMM protease
Function / homology
Function and homology information


polyubiquitin modification-dependent protein binding / proteasome complex / metallopeptidase activity / ubiquitin-dependent protein catabolic process / metal ion binding / cytosol
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. / Ubiquitin family ...: / 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. / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-like protein / 26S proteasome regulatory subunit N11-like protein
Similarity search - Component
Biological speciesCandidatus Caldiarchaeum subterraneum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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
DepositionFeb 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 26S proteasome regulatory subunit N11-like protein
B: 26S proteasome regulatory subunit N11-like protein
C: Ubiquitin-like protein
D: Ubiquitin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1778
Polymers56,8544
Non-polymers3234
Water6,630368
1
A: 26S proteasome regulatory subunit N11-like protein
C: Ubiquitin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5884
Polymers28,4272
Non-polymers1612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-80 kcal/mol
Surface area12060 Å2
MethodPISA
2
B: 26S proteasome regulatory subunit N11-like protein
D: Ubiquitin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5884
Polymers28,4272
Non-polymers1612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-60 kcal/mol
Surface area11890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.674, 94.571, 170.855
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 17061.760 Da / Num. of mol.: 2
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, ubiquitinyl hydrolase 1
#2: Protein Ubiquitin-like protein


Mass: 11365.131 Da / Num. of mol.: 2
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
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 368 / 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: 3.01 Å3/Da / Density % sol: 59.11 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 100 mM sodium acetate, pH 4.6, 1.5 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.283 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.283 Å / Relative weight: 1
ReflectionResolution: 1.85→37.9 Å / Num. obs: 58917 / % possible obs: 99.6 % / Redundancy: 12.9 % / CC1/2: 1 / Rmerge(I) obs: 0.074 / Net I/σ(I): 19.8
Reflection shellResolution: 1.85→1.96 Å / Redundancy: 12.9 % / Rmerge(I) obs: 0.779 / Mean I/σ(I) obs: 2.66 / Num. unique obs: 9241 / CC1/2: 0.9 / % possible all: 97.9

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Processing

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

6fjv


Resolution: 1.85→37.9 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / SU B: 4.949 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.102 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20058 2946 5 %RANDOM
Rwork0.17269 ---
obs0.17409 55970 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 41.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å2-0 Å2-0 Å2
2---1.78 Å20 Å2
3---2.24 Å2
Refinement stepCycle: 1 / Resolution: 1.85→37.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3631 0 12 368 4011
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193792
X-RAY DIFFRACTIONr_bond_other_d0.0010.023758
X-RAY DIFFRACTIONr_angle_refined_deg1.3851.9855164
X-RAY DIFFRACTIONr_angle_other_deg0.72438660
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8955500
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.82523.615130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.34915649
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1171520
X-RAY DIFFRACTIONr_chiral_restr0.0780.2614
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214236
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02782
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_it1.3722.3051970
X-RAY DIFFRACTIONr_mcbond_other1.3732.3051969
X-RAY DIFFRACTIONr_mcangle_it2.0913.4472465
X-RAY DIFFRACTIONr_mcangle_other2.0923.4472466
X-RAY DIFFRACTIONr_scbond_it2.1462.6041822
X-RAY DIFFRACTIONr_scbond_other2.1462.6041822
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4083.7822694
X-RAY DIFFRACTIONr_long_range_B_refined7.61920.6034511
X-RAY DIFFRACTIONr_long_range_B_other7.44319.4844324
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.846→1.894 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 206 -
Rwork0.398 3928 -
obs--95.69 %
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)
12.39751.2441-0.42342.8683-0.12774.69940.01720.12180.1177-0.03680.0210.1841-0.0018-0.2314-0.03820.0544-0.03950.00710.0481-0.00220.01426.730828.484912.7255
23.2910.1505-1.35372.78531.05113.06590.08730.13910.23020.00120.00010.2379-0.1012-0.187-0.08750.0869-0.07620.00710.09880.01580.0382-14.844111.854720.8901
38.62822.3988-0.1610.7905-3.415810.03530.0401-0.17880.41280.5159-0.0649-0.4344-1.13590.08280.02470.22640.0684-0.0180.1719-0.09920.187748.605535.2365-2.7435
47.38451.3352-0.97476.0765-6.163313.0183-0.17440.60730.0051-0.50930.26340.287-0.1823-0.2025-0.0890.24060.0847-0.00790.19460.02980.1999-33.674-22.732550.0527
55.43392.00680.02283.23790.82862.45260.020.1108-0.41220.05050.1196-0.43380.17520.3831-0.13960.104-0.0420.00590.1169-0.03670.066630.700531.942411.5583
63.40822.3982-0.49374.9929-0.86943.12110.3164-0.4894-0.28740.7726-0.3388-0.34130.03940.13980.02240.2669-0.1492-0.01560.1644-0.00120.0666-22.8497-6.145135.604
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 148
2X-RAY DIFFRACTION2B-3 - 148
3X-RAY DIFFRACTION3C-11 - 0
4X-RAY DIFFRACTION4D-11 - 0
5X-RAY DIFFRACTION5C1 - 78
6X-RAY DIFFRACTION6D1 - 78

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