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- PDB-3eay: Crystal structure of the human SENP7 catalytic domain -

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Basic information

Entry
Database: PDB / ID: 3eay
TitleCrystal structure of the human SENP7 catalytic domain
ComponentsSentrin-specific protease 7
KeywordsHYDROLASE / protease / sentrin-specific protease / ULP / SENP / SUMO / ubiquitin / crystal / Alternative splicing / Phosphoprotein / Polymorphism / Thiol protease / Ubl conjugation pathway
Function / homology
Function and homology information


SUMO-specific endopeptidase activity / protein desumoylation / antiviral innate immune response / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / proteolysis / nucleus / cytoplasm
Similarity search - Function
Actin-binding Protein, T-fimbrin; domain 1 - #20 / Ubiquitin-related / Ubiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain / Ulp1 protease family, C-terminal catalytic domain / Actin-binding Protein, T-fimbrin; domain 1 / TATA-Binding Protein / Papain-like cysteine peptidase superfamily / 2-Layer Sandwich / Orthogonal Bundle ...Actin-binding Protein, T-fimbrin; domain 1 - #20 / Ubiquitin-related / Ubiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain / Ulp1 protease family, C-terminal catalytic domain / Actin-binding Protein, T-fimbrin; domain 1 / TATA-Binding Protein / Papain-like cysteine peptidase superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Sentrin-specific protease 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.4 Å
AuthorsLima, C.D. / Reverter, D.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structure of the Human SENP7 Catalytic Domain and Poly-SUMO Deconjugation Activities for SENP6 and SENP7.
Authors: Lima, C.D. / Reverter, D.
History
DepositionAug 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Sentrin-specific protease 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9342
Polymers37,8381
Non-polymers961
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.220, 76.220, 103.460
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Sentrin-specific protease 7 / Sentrin/SUMO-specific protease SENP7


Mass: 37837.848 Da / Num. of mol.: 1 / Fragment: Catalytic domain: Residues 662-984
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SENP7, KIAA1707, SSP2, SUSP2 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CP(RIL)
References: UniProt: Q9BQF6, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.29 Å3/Da / Density % sol: 46.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: The reservoir solution contained 1.6 M ammonium sulfate and 100 mM sodium citrate pH 6.5. Single crystals appeared after 2 days from equal volumes of protein solution (10 mg/ml in 5 mM Tris- ...Details: The reservoir solution contained 1.6 M ammonium sulfate and 100 mM sodium citrate pH 6.5. Single crystals appeared after 2 days from equal volumes of protein solution (10 mg/ml in 5 mM Tris-HCl pH 8.0, 25 mM NaCl) and reservoir solution, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 10, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 14050 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.5 % / Rmerge(I) obs: 0.065 / Χ2: 1.049 / Net I/σ(I): 15.9
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 4 / Num. unique all: 1380 / Χ2: 0.735 / % possible all: 99.9

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Phasing

PhasingMethod: MIR

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
CNS1.2refinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MIR / Resolution: 2.4→35.76 Å / Rfactor Rfree error: 0.01 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.821 / Data cutoff high absF: 1900543 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.256 688 4.9 %RANDOM
Rwork0.202 ---
obs-13903 98.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.36 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso max: 107.86 Å2 / Biso mean: 51.342 Å2 / Biso min: 20.49 Å2
Baniso -1Baniso -2Baniso -3
1-9.41 Å20 Å20 Å2
2--9.41 Å20 Å2
3----18.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.4→35.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2058 0 5 66 2129
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it2.052
X-RAY DIFFRACTIONc_mcangle_it3.352.5
X-RAY DIFFRACTIONc_scbond_it3.963
X-RAY DIFFRACTIONc_scangle_it5.644
LS refinement shellResolution: 2.4→2.49 Å / Rfactor Rfree error: 0.045 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.359 63 4.7 %
Rwork0.309 1277 -
all-1340 -
obs-999 96.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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