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- PDB-2iyc: SENP1 native structure -

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Basic information

Entry
Database: PDB / ID: 2iyc
TitleSENP1 native structure
ComponentsSENTRIN-SPECIFIC PROTEASE 1
KeywordsHYDROLASE / PROTEASE / THIOL PROTEASE / NUCLEAR PROTEIN / UBL CONJUGATION PATHWAY
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: 2.45 Å
AuthorsDong, C. / Naismith, J.H.
Citation
Journal: To be Published
Title: Senp1 Native Structure
Authors: Dong, C. / Naismith, J.H.
#1: Journal: Biochem.J. / Year: 2006
Title: The Structure of Senp1 Sumo-2 Co-Complex Suggests a Structural Basis for Discrimination between Sumo Paralogues During Processing
Authors: Shen, L. / Dong, C. / Liu, H. / Naismith, J.H. / Hay, R.T.
History
DepositionJul 14, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ncs_dom_lim
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 / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)53,8642
Polymers53,8642
Non-polymers00
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 2 / Auth seq-ID: 430 - 640 / Label seq-ID: 12 - 222

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

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Components

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


Mass: 26932.211 Da / Num. of mol.: 2 / Fragment: CATALYTIC FRAGMENT, RESIDUES 419-643
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q9P0U3, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE EXTRA RESIDUE AT POSITION 593 IN CHAINS A AND B IS A KNOWN CONFLICT IN UNIPROT AND IS DESCRIBED ...THE EXTRA RESIDUE AT POSITION 593 IN CHAINS A AND B IS A KNOWN CONFLICT IN UNIPROT AND IS DESCRIBED IN PUBMED ID: 12477932.

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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: 2.77 Å3/Da / Density % sol: 55.22 %

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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→54 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 / Redundancy: 9 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→53 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.912 / SU B: 20.526 / SU ML: 0.229 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.422 / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.THIS REPLACES PREVIOUS ENTRY WHICH WHICH HAD SEQUENCE CONFLICTS. THE BOND DEVIATIONS FOR GLU AND HIS ARE CAUSED BY DENSITY ON THE SYMMETRY ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.THIS REPLACES PREVIOUS ENTRY WHICH WHICH HAD SEQUENCE CONFLICTS. THE BOND DEVIATIONS FOR GLU AND HIS ARE CAUSED BY DENSITY ON THE SYMMETRY POSITION. THIS SUCKS THE SIDE CHAINS IN. A WATER HERE IS REJECTED BY ARWARP ETC.
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1136 4.9 %RANDOM
Rwork0.217 ---
obs0.219 21832 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.97 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20.08 Å20 Å2
2--0.15 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 2.45→53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3782 0 0 90 3872
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223868
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4831.945202
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.245450
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.16324.242198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.04315746
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5651524
X-RAY DIFFRACTIONr_chiral_restr0.0990.2552
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022902
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2320.21801
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.22628
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2179
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3820.291
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3550.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5761.52324
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.89223660
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.67231768
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4824.51542
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
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
844tight positional0.060.05
915medium positional0.530.5
844tight thermal0.110.5
915medium thermal0.772
LS refinement shellResolution: 2.45→2.51 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.328 87
Rwork0.296 1557
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)
15.67730.2597-1.23972.98560.18974.16190.2845-0.33460.26420.2679-0.07950.2677-0.1451-0.051-0.2049-0.0796-0.03140.1534-0.3381-0.0812-0.232728.0233-9.6528-6.2222
25.60094.0183-2.09216.9026-2.69287.3873-0.2788-0.0475-0.6864-0.5649-0.0426-1.1643-0.22160.7850.3214-0.0111-0.10860.1726-0.15980.0456-0.081336.6469-16.968725.0269
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A419 - 644
2X-RAY DIFFRACTION2B419 - 644

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