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- PDB-8b0u: Structure of the CalpL/T10 complex -

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Basic information

Entry
Database: PDB / ID: 8b0u
TitleStructure of the CalpL/T10 complex
Components
  • CalpT10
  • SAVED domain-containing protein
KeywordsHYDROLASE / Protease / CRISPR type III / cOA / cA4 / peptide binding protein
Function / homologySMODS-associated and fused to various effectors / SMODS-associated and fused to various effectors sensor domain / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / membrane / DUF4388 domain-containing protein / SMODS-associated and fused to various effectors domain-containing protein
Function and homology information
Biological speciesSulfurihydrogenibium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.29 Å
AuthorsSchneberger, N. / Hagelueken, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)HA 6805/6-1 Germany
CitationJournal: Nature / Year: 2023
Title: Antiviral signalling by a cyclic nucleotide activated CRISPR protease.
Authors: Rouillon, C. / Schneberger, N. / Chi, H. / Blumenstock, K. / Da Vela, S. / Ackermann, K. / Moecking, J. / Peter, M.F. / Boenigk, W. / Seifert, R. / Bode, B.E. / Schmid-Burgk, J.L. / Svergun, ...Authors: Rouillon, C. / Schneberger, N. / Chi, H. / Blumenstock, K. / Da Vela, S. / Ackermann, K. / Moecking, J. / Peter, M.F. / Boenigk, W. / Seifert, R. / Bode, B.E. / Schmid-Burgk, J.L. / Svergun, D. / Geyer, M. / White, M.F. / Hagelueken, G.
History
DepositionSep 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2023Group: Database references / Structure summary / Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _struct.title
Revision 1.2Feb 8, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SAVED domain-containing protein
D: CalpT10
B: SAVED domain-containing protein
C: CalpT10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,99613
Polymers133,1394
Non-polymers8579
Water362
1
A: SAVED domain-containing protein
D: CalpT10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1388
Polymers66,5702
Non-polymers5686
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SAVED domain-containing protein
C: CalpT10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8585
Polymers66,5702
Non-polymers2883
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.754, 96.598, 131.710
Angle α, β, γ (deg.)90.00, 98.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SAVED domain-containing protein


Mass: 57813.680 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: CalpL protease / Source: (gene. exp.) Sulfurihydrogenibium (bacteria) / Strain: YO3AOP1 / Gene: SYO3AOP1_0656 / Production host: Escherichia coli (E. coli) / References: UniProt: B2V8L9
#2: Protein CalpT10


Mass: 8755.967 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: This is the C-terminal fragment of CalpT that remains after cleavage by CalpL
Source: (gene. exp.) Sulfurihydrogenibium (bacteria) / Strain: YO3AOP1 / Gene: SYO3AOP1_0655 / Production host: Escherichia coli (E. coli) / References: UniProt: B2V8L8
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 4.24 Å3/Da / Density % sol: 71.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 2 M ammonium sulfate, 0.1 M ammonium cacodylate, 0.2 M NaCl at pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 3.29→49.31 Å / Num. obs: 33777 / % possible obs: 99.12 % / Redundancy: 6.8 % / CC1/2: 0.997 / Net I/σ(I): 9.92
Reflection shellResolution: 3.29→3.408 Å / Redundancy: 6.9 % / Num. unique obs: 3321 / CC1/2: 0.467 / % possible all: 99.34

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Processing

SoftwareName: PHASER / Classification: phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7QDA

7qda


Resolution: 3.29→49.31 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2301 1998 5.92 %
Rwork0.195 --
obs0.197 33758 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.29→49.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9392 0 47 2 9441
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029600
X-RAY DIFFRACTIONf_angle_d0.53312950
X-RAY DIFFRACTIONf_dihedral_angle_d13.3633682
X-RAY DIFFRACTIONf_chiral_restr0.0451480
X-RAY DIFFRACTIONf_plane_restr0.0041630
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.29-3.370.34581400.31842236X-RAY DIFFRACTION99
3.37-3.460.36561430.30152266X-RAY DIFFRACTION99
3.46-3.570.36381410.27622236X-RAY DIFFRACTION99
3.57-3.680.31391400.26222221X-RAY DIFFRACTION98
3.68-3.810.29541400.24142240X-RAY DIFFRACTION99
3.81-3.960.2761440.23322279X-RAY DIFFRACTION100
3.96-4.140.25361440.19972290X-RAY DIFFRACTION100
4.14-4.360.23341420.17412267X-RAY DIFFRACTION100
4.36-4.640.20811450.1632282X-RAY DIFFRACTION100
4.64-4.990.19541430.16322279X-RAY DIFFRACTION99
4.99-5.50.21891400.17232237X-RAY DIFFRACTION98
5.5-6.290.26261460.19062305X-RAY DIFFRACTION100
6.29-7.920.21931430.19492282X-RAY DIFFRACTION99
7.92-49.310.1571470.16562340X-RAY DIFFRACTION98

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