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- PDB-2xre: Detection of cobalt in previously unassigned human SENP1 structure -

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Basic information

Entry
Database: PDB / ID: 2xre
TitleDetection of cobalt in previously unassigned human SENP1 structure
ComponentsSENTRIN-SPECIFIC PROTEASE 1
KeywordsHYDROLASE / CYSTEINE PROTEASE
Function / homology
Function and homology information


regulation of definitive erythrocyte differentiation / SUMO-specific endopeptidase activity / deSUMOylase activity / protein desumoylation / SUMO is proteolytically processed / RHOF GTPase cycle / protein sumoylation / regulation of postsynapse assembly / postsynaptic cytosol / presynaptic cytosol ...regulation of definitive erythrocyte differentiation / SUMO-specific endopeptidase activity / deSUMOylase activity / protein desumoylation / SUMO is proteolytically processed / RHOF GTPase cycle / protein sumoylation / regulation of postsynapse assembly / postsynaptic cytosol / presynaptic cytosol / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / regulation of mRNA stability / nuclear membrane / endopeptidase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / focal adhesion / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
Adenoviral Proteinase; Chain / Adenoviral Proteinase; Chain A / Ulp1 protease family, C-terminal catalytic domain / Ubiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain / Papain-like cysteine peptidase superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Sentrin-specific protease 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsRimsa, V. / Eadsforth, T. / Hay, R.T. / Hunter, W.N.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: The Role of Co2+ in the Crystallization of Human Senp1 and Comments on the Limitations of Automated Refinement Protocols
Authors: Rimsa, V. / Eadsforth, T. / Hunter, W.N.
History
DepositionSep 14, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2012Group: Database references / Non-polymer description / Version format compliance
Revision 1.2Oct 3, 2012Group: Derived calculations
Revision 1.3Nov 20, 2013Group: Derived calculations / Source and taxonomy
Revision 1.4May 29, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SENTRIN-SPECIFIC PROTEASE 1
B: SENTRIN-SPECIFIC PROTEASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,73713
Polymers54,7572
Non-polymers98011
Water1,09961
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-8.3 kcal/mol
Surface area21920 Å2
MethodPISA
2
B: SENTRIN-SPECIFIC PROTEASE 1
hetero molecules

A: SENTRIN-SPECIFIC PROTEASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,73713
Polymers54,7572
Non-polymers98011
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z+1/31
Buried area3210 Å2
ΔGint-9.5 kcal/mol
Surface area21700 Å2
MethodPISA
3
A: SENTRIN-SPECIFIC PROTEASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7475
Polymers27,3791
Non-polymers3684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
B: SENTRIN-SPECIFIC PROTEASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9908
Polymers27,3791
Non-polymers6117
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.981, 71.981, 200.640
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein SENTRIN-SPECIFIC PROTEASE 1 / SENTRIN/SUMO-SPECIFIC PROTEASE SENP1


Mass: 27378.580 Da / Num. of mol.: 2 / Fragment: CATALYTIC FRAGMENT, RESIDUES 415-644
Source method: isolated from a genetically manipulated source
Details: COBALT(II) ION, GLYCEROL / Source: (gene. exp.) HOMO SAPIENS (human) / Cell line: ESCHERICHIA COLI / Plasmid: PHISTEV30A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD
References: UniProt: Q9P0U3, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.11 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop
Details: CRYSTALLIZATION WAS PERFORMED USING A SITTING-DROP VAPOUR-DIFFUSION METHOD. CRYSTALS APPEARED FROM EQUAL VOLUMES OF PROTEIN SOLUTION (20 MG/ML IN 20 MM TRIS/HCL, PH 8.0, AND 50 MM NACL) AND ...Details: CRYSTALLIZATION WAS PERFORMED USING A SITTING-DROP VAPOUR-DIFFUSION METHOD. CRYSTALS APPEARED FROM EQUAL VOLUMES OF PROTEIN SOLUTION (20 MG/ML IN 20 MM TRIS/HCL, PH 8.0, AND 50 MM NACL) AND RESERVOIR SOLUTION CONTAINING 100 MM COCL2, 0.1M MES, PH 6.5, AND 1.8 M (NH4)2SO4.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.45→45.6 Å / Num. obs: 21832 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 19
Reflection shellResolution: 2.45→2.51 Å / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IYC

2iyc


Resolution: 2.45→45.6 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.874 / SU B: 11.596 / SU ML: 0.27 / Cross valid method: THROUGHOUT / ESU R: 0.479 / ESU R Free: 0.337 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.317 1136 4.9 %RANDOM
Rwork0.237 ---
obs0.241 21829 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.36 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.45→45.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3705 0 61 61 3827
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223990
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5251.9445379
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3045477
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.53223.98201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.30815728
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2021526
X-RAY DIFFRACTIONr_chiral_restr0.1070.2558
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213026
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.0732316
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.71653760
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.72771674
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.856101614
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.45→2.51 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 87 -
Rwork0.331 1555 -
obs--100 %

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