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- PDB-5ln5: Crystal structure of the Wss1 E203Q mutant from S. pombe -

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Basic information

Entry
Database: PDB / ID: 5ln5
TitleCrystal structure of the Wss1 E203Q mutant from S. pombe
ComponentsUbiquitin and WLM domain-containing metalloprotease SPCC1442.07c
KeywordsHYDROLASE / Metalloprotease / DNA-Repair / Endoprotease / Regulation / Mutant
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / proteasome binding / protein sumoylation / transition metal ion binding / metallopeptidase activity / single-stranded DNA binding / double-stranded DNA binding / DNA repair / proteolysis / zinc ion binding ...Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / proteasome binding / protein sumoylation / transition metal ion binding / metallopeptidase activity / single-stranded DNA binding / double-stranded DNA binding / DNA repair / proteolysis / zinc ion binding / nucleus / cytosol
Similarity search - Function
WLM domain / WLM domain / WLM domain profile. / Neutral zinc metallopeptidases, zinc-binding region signature. / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
CARBONATE ION / NICKEL (II) ION / DNA-dependent metalloprotease WSS1 homolog 2
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsGroll, M. / Stingele, J. / Boulton, S.J.
CitationJournal: Mol.Cell / Year: 2016
Title: Mechanism and Regulation of DNA-Protein Crosslink Repair by the DNA-Dependent Metalloprotease SPRTN.
Authors: Stingele, J. / Bellelli, R. / Alte, F. / Hewitt, G. / Sarek, G. / Maslen, S.L. / Tsutakawa, S.E. / Borg, A. / Kjr, S. / Tainer, J.A. / Skehel, J.M. / Groll, M. / Boulton, S.J.
History
DepositionAug 3, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin and WLM domain-containing metalloprotease SPCC1442.07c
B: Ubiquitin and WLM domain-containing metalloprotease SPCC1442.07c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3935
Polymers30,2162
Non-polymers1773
Water2,540141
1
A: Ubiquitin and WLM domain-containing metalloprotease SPCC1442.07c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2273
Polymers15,1081
Non-polymers1192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin and WLM domain-containing metalloprotease SPCC1442.07c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1672
Polymers15,1081
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.160, 57.260, 50.640
Angle α, β, γ (deg.)90.00, 113.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ubiquitin and WLM domain-containing metalloprotease SPCC1442.07c / DNA-dependent Metalloprotease SPRTN


Mass: 15107.933 Da / Num. of mol.: 2 / Fragment: UNP residues 107-233 / Mutation: E203Q
Source method: isolated from a genetically manipulated source
Details: Used construct was a truncation and E203Q mutant of SPCC1442.07c
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: SPCC1442.07c / Plasmid: pRSETA / Details (production host): pRSETA / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O94580, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-CO3 / CARBONATE ION / Carbonate


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 1.82 Å3/Da / Density % sol: 32.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100 mM TRIS/HCl, 20% PEG 1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. obs: 20977 / % possible obs: 95.3 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 14.1
Reflection shellResolution: 1.75→1.85 Å / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 2.7 / % possible all: 94.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JIG

5jig


Resolution: 1.75→15 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.971 / SU B: 5.9 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.356 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19541 1049 5 %RANDOM
Rwork0.17256 ---
obs0.17404 19928 95.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.41 Å2
Baniso -1Baniso -2Baniso -3
1--2.09 Å20 Å2-0.11 Å2
2--1.38 Å20 Å2
3---0.56 Å2
Refinement stepCycle: LAST / Resolution: 1.75→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1893 0 6 141 2040
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0191940
X-RAY DIFFRACTIONr_bond_other_d0.0020.021829
X-RAY DIFFRACTIONr_angle_refined_deg0.9651.9392618
X-RAY DIFFRACTIONr_angle_other_deg0.734187
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9145221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.42822.642106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.01215346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0761520
X-RAY DIFFRACTIONr_chiral_restr0.0570.2283
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022149
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02491
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_it2.2492.808896
X-RAY DIFFRACTIONr_mcbond_other2.2392.806895
X-RAY DIFFRACTIONr_mcangle_it2.5294.1961113
X-RAY DIFFRACTIONr_mcangle_other2.5284.1981114
X-RAY DIFFRACTIONr_scbond_it2.3963.4821044
X-RAY DIFFRACTIONr_scbond_other2.3833.4781042
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.464.991503
X-RAY DIFFRACTIONr_long_range_B_refined3.59724.6942263
X-RAY DIFFRACTIONr_long_range_B_other3.28624.2992220
X-RAY DIFFRACTIONr_rigid_bond_restr1.24233769
X-RAY DIFFRACTIONr_sphericity_free24.799554
X-RAY DIFFRACTIONr_sphericity_bonded6.91153815
LS refinement shellResolution: 1.75→1.794 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 75 -
Rwork0.241 1427 -
obs--95.3 %
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)
12.3132-0.514-0.10240.1324-0.05490.70160.10010.2142-0.1372-0.0257-0.08320.0390.02880.0198-0.01690.01870.0052-0.01280.0622-0.02580.0268-1.0286-7.84846.9087
21.523-0.0383-0.46690.13160.15630.65270.0827-0.14030.02810.0096-0.0580.0031-0.02020.0143-0.02470.0292-0.0123-0.00290.044-0.0080.0128-5.3791-7.9675-19.8069
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 122
2X-RAY DIFFRACTION2B2 - 122

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