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- PDB-6k9n: Rice_OTUB_like_catalytic domain -

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Basic information

Entry
Database: PDB / ID: 6k9n
TitleRice_OTUB_like_catalytic domain
ComponentsUbiquitin thioesterase
KeywordsHYDROLASE / Deubiquitinase
Function / homology
Function and homology information


ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / proteolysis
Similarity search - Function
Peptidase C65 Otubain, subdomain 2 / Peptidase C65 Otubain, subdomain 1 / Peptidase C65, otubain / Peptidase C65, otubain, subdomain 2 / Peptidase C65, otubain, subdomain 1 / Peptidase C65 Otubain / 3 helical TM bundles of succinate and fumarate reductases / OTU domain / OTU domain profile. / Papain-like cysteine peptidase superfamily ...Peptidase C65 Otubain, subdomain 2 / Peptidase C65 Otubain, subdomain 1 / Peptidase C65, otubain / Peptidase C65, otubain, subdomain 2 / Peptidase C65, otubain, subdomain 1 / Peptidase C65 Otubain / 3 helical TM bundles of succinate and fumarate reductases / OTU domain / OTU domain profile. / Papain-like cysteine peptidase superfamily / Phosphorylase Kinase; domain 1 / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ubiquitinyl hydrolase 1
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsLu, L.N. / Liu, L. / Wang, F.
Funding support China, 7items
OrganizationGrant numberCountry
The National Key Research and Development Program of China2017YFD0500400 China
The National Key Research and Development Program of China2016YFC0906000 China
National Natural Science Foundation of China (NSFC)32071269 China
National Natural Science Foundation of China (NSFC)31770827 China
National Natural Science Foundation of China (NSFC)21736002 China
National Natural Science Foundation of China (NSFC)31640016 China
National Natural Science Foundation of China (NSFC)31500980 China
CitationJournal: Nat Commun / Year: 2022
Title: Met1-specific motifs conserved in OTUB subfamily of green plants enable rice OTUB1 to hydrolyse Met1 ubiquitin chains
Authors: Lu, L. / Zhai, X. / Li, X. / Wang, S. / Zhang, L. / Wang, L. / Jin, X. / Liang, L. / Deng, Z. / Li, Z. / Wang, Y. / Fu, X. / Hu, H. / Wang, J. / Mei, Z. / He, Z. / Wang, F.
History
DepositionJun 17, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 2.0Sep 8, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / cell ...atom_site / cell / database_2 / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_audit_support / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / software / struct_conf / struct_mon_prot_cis / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range / symmetry
Item: _cell.volume / _database_2.pdbx_DOI ..._cell.volume / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_number_of_molecules / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_high / _refine.ls_d_res_low / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.d_res_high / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_restr.type / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_R_free / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.percent_reflns_obs / _reflns.B_iso_Wilson_estimate / _software.version / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _symmetry.space_group_name_Hall
Description: Real space R-factor / Provider: author / Type: Coordinate replacement
Revision 2.1Nov 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 2.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin thioesterase
B: Ubiquitin thioesterase
C: Ubiquitin thioesterase
D: Ubiquitin thioesterase


Theoretical massNumber of molelcules
Total (without water)114,1654
Polymers114,1654
Non-polymers00
Water8,503472
1
A: Ubiquitin thioesterase


Theoretical massNumber of molelcules
Total (without water)28,5411
Polymers28,5411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin thioesterase


Theoretical massNumber of molelcules
Total (without water)28,5411
Polymers28,5411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ubiquitin thioesterase


Theoretical massNumber of molelcules
Total (without water)28,5411
Polymers28,5411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ubiquitin thioesterase


Theoretical massNumber of molelcules
Total (without water)28,5411
Polymers28,5411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.688, 144.810, 155.848
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein
Ubiquitin thioesterase / Ubiquitinyl hydrolase 1


Mass: 28541.180 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: OsJ_28104 / Production host: Escherichia coli (E. coli) / References: UniProt: B9G207, ubiquitinyl hydrolase 1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 472 / 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: 2.93 Å3/Da / Density % sol: 58.09 %
Crystal growTemperature: 291 K / Method: evaporation
Details: 0.15 M Potassium bromide, 30% w/v Polyethylene glycol monomethyl ether 2,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9873 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 62083 / % possible obs: 99.7 % / Redundancy: 10.8 % / Biso Wilson estimate: 36.05 Å2 / Rpim(I) all: 0.035 / Net I/σ(I): 7.54
Reflection shellResolution: 2.25→2.29 Å / Num. unique obs: 3018 / Rpim(I) all: 0.158

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZFY

2zfy


Resolution: 2.27→47.38 Å / SU ML: 0.2162 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.0378
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.217 3028 4.89 %
Rwork0.1864 58904 -
obs0.1879 61932 98.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.71 Å2
Refinement stepCycle: LAST / Resolution: 2.27→47.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7806 0 0 472 8278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047974
X-RAY DIFFRACTIONf_angle_d0.717110754
X-RAY DIFFRACTIONf_chiral_restr0.04511168
X-RAY DIFFRACTIONf_plane_restr0.00581400
X-RAY DIFFRACTIONf_dihedral_angle_d5.10611050
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.310.2971970.20341783X-RAY DIFFRACTION66.13
2.31-2.350.24971600.20492659X-RAY DIFFRACTION99.79
2.35-2.390.29881370.20872703X-RAY DIFFRACTION99.86
2.39-2.430.24821160.20912680X-RAY DIFFRACTION99.86
2.43-2.480.26131440.21232718X-RAY DIFFRACTION99.83
2.48-2.530.27351450.21842642X-RAY DIFFRACTION99.39
2.53-2.580.25531420.21182700X-RAY DIFFRACTION99.79
2.58-2.640.23731350.19392682X-RAY DIFFRACTION99.82
2.64-2.710.2291320.1952728X-RAY DIFFRACTION99.76
2.71-2.780.21891320.20542690X-RAY DIFFRACTION99.75
2.78-2.860.23741500.2082701X-RAY DIFFRACTION99.89
2.86-2.960.2421190.20722727X-RAY DIFFRACTION99.86
2.96-3.060.23431300.19772707X-RAY DIFFRACTION99.86
3.06-3.180.19711320.19852734X-RAY DIFFRACTION99.72
3.18-3.330.2151410.20382729X-RAY DIFFRACTION99.65
3.33-3.50.22191370.19062714X-RAY DIFFRACTION99.96
3.5-3.720.21091550.18562737X-RAY DIFFRACTION99.83
3.72-4.010.2091280.16542751X-RAY DIFFRACTION99.69
4.01-4.410.16661340.14872744X-RAY DIFFRACTION99.93
4.41-5.050.18391640.14882755X-RAY DIFFRACTION99.29
5.05-6.360.23921500.19262780X-RAY DIFFRACTION99.59
6.36-47.380.19851480.19072840X-RAY DIFFRACTION95.95

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