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- PDB-6fju: Rpn11 homolog from Caldiarchaeum Subterraneum -

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Basic information

Entry
Database: PDB / ID: 6fju
TitleRpn11 homolog from Caldiarchaeum Subterraneum
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
: / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile.
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: 1.65 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 ...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 / struct_ncs_dom_lim
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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
B: 26S proteasome regulatory subunit N11-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4605
Polymers51,2332
Non-polymers2273
Water4,414245
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-119 kcal/mol
Surface area16610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.452, 65.614, 99.708
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 0 - 174 / Label seq-ID: 26 - 200

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 25616.539 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
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.06 Å3/Da / Density % sol: 40.22 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 100 mM HEPES pH 7.0, 15% 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: Apr 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→33.8 Å / Num. obs: 51685 / % possible obs: 99.7 % / Redundancy: 6.86 % / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Net I/σ(I): 18.8
Reflection shellResolution: 1.65→1.75 Å / Redundancy: 6.29 % / Rmerge(I) obs: 0.973 / Mean I/σ(I) obs: 1.77 / CC1/2: 0.791 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OCL

4ocl


Resolution: 1.65→33.8 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.556 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.079 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19025 2585 5 %RANDOM
Rwork0.16576 ---
obs0.16698 49099 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.662 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å2-0 Å20 Å2
2---1.28 Å20 Å2
3---0.45 Å2
Refinement stepCycle: 1 / Resolution: 1.65→33.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2713 0 7 245 2965
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0192868
X-RAY DIFFRACTIONr_bond_other_d0.0070.022839
X-RAY DIFFRACTIONr_angle_refined_deg1.891.9613903
X-RAY DIFFRACTIONr_angle_other_deg1.31636531
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0495374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.79123.036112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.67115512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3821516
X-RAY DIFFRACTIONr_chiral_restr0.1250.2456
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023182
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02650
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_it2.0751.9141424
X-RAY DIFFRACTIONr_mcbond_other2.0631.9131423
X-RAY DIFFRACTIONr_mcangle_it3.0352.8561783
X-RAY DIFFRACTIONr_mcangle_other3.0352.8561784
X-RAY DIFFRACTIONr_scbond_it2.9862.2911444
X-RAY DIFFRACTIONr_scbond_other2.9722.2831441
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5493.2772102
X-RAY DIFFRACTIONr_long_range_B_refined7.85217.1833381
X-RAY DIFFRACTIONr_long_range_B_other7.75416.5583287
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 10008 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.647→1.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 182 -
Rwork0.295 3445 -
obs--96.59 %
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)
11.75740.05160.14953.18020.56951.6768-0.05770.12510.1649-0.223-0.06770.093-0.2123-0.00820.12540.03960.0036-0.02570.01160.00740.027527.740335.987710.3022
22.52590.79250.45853.55410.45251.92420.11470.0392-0.2784-0.2563-0.0235-0.0790.30880.0765-0.09120.09110.0093-0.02820.01720.00620.04323.10717.55385.0633
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 175
2X-RAY DIFFRACTION2B0 - 174

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