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- PDB-6wxx: crystal structure of cA4-activated Card1 -

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Basic information

Entry
Database: PDB / ID: 6wxx
Titlecrystal structure of cA4-activated Card1
Components
  • Card1
  • cA4
KeywordsDNA BINDING PROTEIN/RNA / Card1 / Dnase / cyclic oligoadenylates / DNA BINDING PROTEIN / DNA BINDING PROTEIN-RNA complex
Function / homologyProtein of unknown function DUF1887 / Domain of unknown function (DUF1887) / tRNA endonuclease-like domain superfamily / Restriction endonuclease type II-like / nucleic acid binding / : / RNA / Card1 domain-containing protein
Function and homology information
Biological speciesTreponema succinifaciens
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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
B: Card1
A: Card1
D: Card1
C: Card1
Y: cA4
X: cA4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,81610
Polymers182,5966
Non-polymers2204
Water0
1
B: Card1
A: Card1
X: cA4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,4085
Polymers91,2983
Non-polymers1102
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5670 Å2
ΔGint-25 kcal/mol
Surface area33370 Å2
MethodPISA
2
D: Card1
C: Card1
Y: cA4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,4085
Polymers91,2983
Non-polymers1102
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-27 kcal/mol
Surface area33880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.064, 121.216, 103.708
Angle α, β, γ (deg.)90.000, 113.061, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Card1


Mass: 45013.043 Da / Num. of mol.: 4
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
#2: RNA chain cA4


Mass: 1271.866 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.76 Å3/Da / Density % sol: 55.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1 M citric acid, 10% PEG6000 (v/v), final pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 38486 / % possible obs: 98.68 % / Redundancy: 3.9 % / Biso Wilson estimate: 79.98 Å2 / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.1426 / Rpim(I) all: 0.08202 / Rrim(I) all: 0.165 / Net I/σ(I): 8.06
Reflection shellResolution: 3→3.107 Å / Rmerge(I) obs: 1.215 / Mean I/σ(I) obs: 1.06 / Num. unique obs: 38486 / CC1/2: 0.457 / CC star: 0.792 / Rpim(I) all: 0.7261 / Rrim(I) all: 1.421

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Processing

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

Resolution: 3→28.88 Å / SU ML: 0.4736 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.8868
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2373 1886 4.92 %
Rwork0.2037 36481 -
obs0.2053 38367 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 78.15 Å2
Refinement stepCycle: LAST / Resolution: 3→28.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12368 176 4 0 12548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006412826
X-RAY DIFFRACTIONf_angle_d0.803117332
X-RAY DIFFRACTIONf_chiral_restr0.17741888
X-RAY DIFFRACTIONf_plane_restr0.00432184
X-RAY DIFFRACTIONf_dihedral_angle_d19.27894834
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.080.37531410.32192797X-RAY DIFFRACTION98.66
3.08-3.170.3361350.3082768X-RAY DIFFRACTION98.01
3.17-3.270.32191500.28642838X-RAY DIFFRACTION99.43
3.27-3.390.30911390.28252783X-RAY DIFFRACTION99.05
3.39-3.530.31911530.2582786X-RAY DIFFRACTION98.99
3.53-3.690.28361460.24052811X-RAY DIFFRACTION99.16
3.69-3.880.29511420.2362814X-RAY DIFFRACTION99.03
3.88-4.120.26441490.20362756X-RAY DIFFRACTION97.55
4.12-4.440.18061460.17232817X-RAY DIFFRACTION99.33
4.44-4.880.18631480.15912808X-RAY DIFFRACTION99.56
4.89-5.590.20461480.17482834X-RAY DIFFRACTION99.5
5.59-7.020.24411460.20732828X-RAY DIFFRACTION98.25
7.03-28.880.18061430.15822841X-RAY DIFFRACTION97.93

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