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- PDB-6wxy: crystal structure of cA6-bound Card1 -

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Basic information

Entry
Database: PDB / ID: 6wxy
Titlecrystal structure of cA6-bound Card1
Components
  • Card1
  • cA6
KeywordsDNA BINDING PROTEIN/RNA / Cad1 / Dnase / cyclic oligoadenylates / DNA BINDING PROTEIN / DNA BINDING PROTEIN-RNA complex
Function / homologyProtein of unknown function DUF1887 / Card1-like, endonuclease domain / tRNA endonuclease-like domain superfamily / Restriction endonuclease type II-like / nucleic acid binding / metal ion binding / RNA / Card1 domain-containing protein
Function and homology information
Biological speciesTreponema succinifaciens
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRostol, J. / Xie, W. / Patel, D.J. / Marraffini, L.
CitationJournal: Nature / Year: 2021
Title: The Card1 nuclease provides defence during type III CRISPR immunity.
Authors: Rostol, J.T. / Xie, W. / Kuryavyi, V. / Maguin, P. / Kao, K. / Froom, R. / Patel, D.J. / Marraffini, L.A.
History
DepositionMay 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Structure summary
Category: citation / entity ...citation / entity / struct / struct_keywords
Item: _citation.title / _entity.pdbx_description ..._citation.title / _entity.pdbx_description / _struct.pdbx_descriptor / _struct.title / _struct_keywords.pdbx_keywords / _struct_keywords.text
Revision 1.2Feb 10, 2021Group: 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.title / _citation.year
Revision 1.3Feb 17, 2021Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Mar 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cA6
B: Card1
C: Card1


Theoretical massNumber of molelcules
Total (without water)91,9563
Polymers91,9563
Non-polymers00
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-12 kcal/mol
Surface area34960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.911, 124.763, 42.259
Angle α, β, γ (deg.)90.000, 96.790, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: RNA chain cA6


Mass: 1930.277 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein Card1


Mass: 45013.043 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema succinifaciens (strain ATCC 33096 / DSM 2489 / 6091) (bacteria)
Strain: ATCC 33096 / DSM 2489 / 6091 / Gene: Tresu_2185 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F2NWD3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.52 Å3/Da / Density % sol: 51.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.2 M NaCl, 0.1 M Na/K phosphate, pH 6.2, and 20% PEG1000 (v/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→85.85 Å / Num. obs: 51025 / % possible obs: 98.41 % / Redundancy: 3.9 % / Biso Wilson estimate: 42.07 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.05782 / Rpim(I) all: 0.03286 / Rrim(I) all: 0.06675 / Net I/σ(I): 15.48
Reflection shellResolution: 2.1→2.178 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.6304 / Mean I/σ(I) obs: 1.98 / Num. unique obs: 4689 / CC1/2: 0.705 / CC star: 0.91 / Rpim(I) all: 0.3677 / Rrim(I) all: 0.7326 / % possible all: 92.05

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Processing

Software
NameVersionClassification
PHENIX1.18_3855refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: apo Cad1

Resolution: 2.1→85.85 Å / SU ML: 0.2626 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.3437
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2447 2519 4.96 %
Rwork0.2062 48249 -
obs0.2081 50768 98.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.18 Å2
Refinement stepCycle: LAST / Resolution: 2.1→85.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6184 132 0 218 6534
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00726463
X-RAY DIFFRACTIONf_angle_d0.94678744
X-RAY DIFFRACTIONf_chiral_restr0.0725954
X-RAY DIFFRACTIONf_plane_restr0.0051094
X-RAY DIFFRACTIONf_dihedral_angle_d19.35272441
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.140.29831180.28752338X-RAY DIFFRACTION87.03
2.14-2.190.29371510.2762680X-RAY DIFFRACTION98.37
2.19-2.230.31941610.26632660X-RAY DIFFRACTION98.71
2.24-2.290.27821330.24692661X-RAY DIFFRACTION98.83
2.29-2.340.3391260.25412744X-RAY DIFFRACTION99.17
2.34-2.410.27411390.2422674X-RAY DIFFRACTION99.01
2.41-2.480.28671650.24432701X-RAY DIFFRACTION99.17
2.48-2.560.27571450.22922633X-RAY DIFFRACTION99.43
2.56-2.650.30071470.22542728X-RAY DIFFRACTION98.7
2.65-2.760.27531280.23232662X-RAY DIFFRACTION98.69
2.76-2.880.27321290.21932748X-RAY DIFFRACTION99.69
2.88-3.030.28551460.21912721X-RAY DIFFRACTION99.48
3.03-3.220.26171450.22132685X-RAY DIFFRACTION99.4
3.22-3.470.22231340.19562735X-RAY DIFFRACTION99.45
3.47-3.820.26321230.18522718X-RAY DIFFRACTION99.02
3.82-4.370.21571390.17972672X-RAY DIFFRACTION98.56
4.37-5.510.19921240.17672747X-RAY DIFFRACTION99.62
5.51-85.850.20911660.20222742X-RAY DIFFRACTION98.95

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