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- PDB-2xph: Crystal structure of human SENP1 with the bound cobalt -

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Basic information

Entry
Database: PDB / ID: 2xph
TitleCrystal structure of human SENP1 with the bound cobalt
ComponentsSENTRIN-SPECIFIC PROTEASE 1
KeywordsHYDROLASE / CYSTEINE PROTEASE / THIOL PROTEASE
Function / homology
Function and homology information


SUMO-specific endopeptidase activity / deSUMOylase activity / protein desumoylation / SUMO is proteolytically processed / RHOF GTPase cycle / protein sumoylation / regulation of postsynapse assembly / regulation of mRNA stability / endopeptidase activity / nuclear membrane ...SUMO-specific endopeptidase activity / deSUMOylase activity / protein desumoylation / SUMO is proteolytically processed / RHOF GTPase cycle / protein sumoylation / regulation of postsynapse assembly / regulation of mRNA stability / endopeptidase activity / nuclear membrane / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / focal adhesion / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / proteolysis / nucleoplasm / nucleus / cytoplasm
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: 2.4 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. / Hay, R.T. / Hunter, W.N.
History
DepositionAug 26, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2012Group: Database references / Non-polymer description / Version format compliance
Revision 1.2Dec 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)56,7749
Polymers56,1632
Non-polymers6117
Water1,26170
1
A: SENTRIN-SPECIFIC PROTEASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5426
Polymers28,0811
Non-polymers4605
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SENTRIN-SPECIFIC PROTEASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2323
Polymers28,0811
Non-polymers1512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.172, 71.172, 199.988
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: 28081.359 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) / Plasmid: PHISTEV30A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) 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.: 6 / 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.: 70 / 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: 2.6 Å3/Da / Density % sol: 52.76 % / Description: NONE
Crystal growDetails: CRYSTALS FORMED FROM 1 TO 1 OF RESERVOIR SOLUTION (1.8 M AMMONIUM SULFATE, 50 MM COCL2 AND 100 MM MES PH 6.5) AND PROTEIN SOLUTION (20 MG/ML IN 20 MM TRIS/HCL (PH 8.0), AND 50 MM NACL).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.977
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 13, 2010
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.4→45 Å / Num. obs: 23808 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Biso Wilson estimate: 53.9 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.5
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

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

2iyc


Resolution: 2.4→66.66 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.886 / SU B: 9.805 / SU ML: 0.235 / Cross valid method: THROUGHOUT / ESU R: 0.409 / ESU R Free: 0.317 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 407-417 IN CHAIN A AND 407-418 IN CHAIN B ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.31339 1217 5.1 %RANDOM
Rwork0.22702 ---
obs0.23137 22537 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.721 Å2
Baniso -1Baniso -2Baniso -3
1-1.24 Å20.62 Å20 Å2
2--1.24 Å20 Å2
3----1.87 Å2
Refinement stepCycle: LAST / Resolution: 2.4→66.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3790 0 37 70 3897
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223880
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6391.9385245
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6965476
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.41923.98201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.87815680
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6591527
X-RAY DIFFRACTIONr_chiral_restr0.1190.2549
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022983
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_it2.42132285
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.23353690
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.39971595
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.495101544
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: 2.4→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 83 -
Rwork0.302 1663 -
obs--99.94 %

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