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- PDB-7qda: Crystal structure of CalpL -

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Basic information

Entry
Database: PDB / ID: 7qda
TitleCrystal structure of CalpL
ComponentsCalpL
KeywordsPEPTIDE BINDING PROTEIN / Protease / CRISPR type III / cOA
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 / TRIETHYLENE GLYCOL / SMODS-associated and fused to various effectors domain-containing protein
Function and homology information
Biological speciesSulfurihydrogenibium sp. YO3AOP1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsSchneberger, N. / Hagelueken, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
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
DepositionNov 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2023Group: Database references / Category: citation / citation_author
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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CalpL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,64711
Polymers58,1421
Non-polymers1,50610
Water4,252236
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Monomer in gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-26 kcal/mol
Surface area22930 Å2
Unit cell
Length a, b, c (Å)68.896, 68.896, 255.379
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein CalpL


Mass: 58141.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfurihydrogenibium sp. YO3AOP1 (bacteria)
Strain: YO3AOP1 / Gene: SYO3AOP1_0656 / Production host: Escherichia coli (E. coli) / References: UniProt: B2V8L9
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 3.02 Å3/Da / Density % sol: 59.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris-Cl pH 8.0, 38.8 % PEG 400, 0.29 M Li2SO4

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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: 0.9795 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→58.1 Å / Num. obs: 41843 / % possible obs: 99.02 % / Redundancy: 2 % / Biso Wilson estimate: 36.42 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.054 / Net I/σ(I): 23.2
Reflection shellResolution: 2.1→2.175 Å / Redundancy: 2 % / Rmerge(I) obs: 0.34 / Num. unique obs: 3732 / CC1/2: 0.705 / CC star: 0.909 / % possible all: 90.28

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
AutoSol1.19.2_4158phasing
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→58.1 Å / SU ML: 0.2557 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.6748
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2276 1996 4.77 %
Rwork0.1926 39847 -
obs0.1943 41843 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.12 Å2
Refinement stepCycle: LAST / Resolution: 2.1→58.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4079 0 95 236 4410
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00254358
X-RAY DIFFRACTIONf_angle_d0.56655871
X-RAY DIFFRACTIONf_chiral_restr0.0428654
X-RAY DIFFRACTIONf_plane_restr0.0035742
X-RAY DIFFRACTIONf_dihedral_angle_d10.2565595
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.31651290.25912456X-RAY DIFFRACTION86.95
2.15-2.210.28861300.25122822X-RAY DIFFRACTION99.53
2.21-2.280.27431350.23712801X-RAY DIFFRACTION99.97
2.28-2.350.28131320.22952818X-RAY DIFFRACTION100
2.35-2.430.2391160.23322890X-RAY DIFFRACTION100
2.43-2.530.23791320.22822848X-RAY DIFFRACTION100
2.53-2.650.25991790.23122815X-RAY DIFFRACTION100
2.65-2.790.24271690.2162790X-RAY DIFFRACTION100
2.79-2.960.27441080.2262906X-RAY DIFFRACTION99.97
2.96-3.190.261490.22342849X-RAY DIFFRACTION100
3.19-3.510.2461370.19872908X-RAY DIFFRACTION100
3.51-4.020.23531550.16592896X-RAY DIFFRACTION100
4.02-5.060.17471670.14442935X-RAY DIFFRACTION100
5.06-58.10.1921580.16883113X-RAY DIFFRACTION99.85
Refinement TLS params.Method: refined / Origin x: -20.8800144097 Å / Origin y: 24.616751459 Å / Origin z: 12.9409313622 Å
111213212223313233
T0.216600515546 Å2-0.0601663668426 Å20.00682033215823 Å2-0.165872285756 Å2-0.0129964962838 Å2--0.293854763824 Å2
L0.332307943828 °20.0536750221987 °2-0.264801632806 °2-0.321077001674 °2-0.548408255524 °2--3.01481003893 °2
S-0.00104523039487 Å °-0.0319267712184 Å °0.0224029541586 Å °0.0374725561689 Å °-0.0172185735881 Å °0.0390995155361 Å °-0.0240836346758 Å °-0.0187452532895 Å °0.0243878040466 Å °
Refinement TLS groupSelection details: all

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