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- PDB-6wxw: crystal structure of apo Card1 -

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Basic information

Entry
Database: PDB / ID: 6wxw
Titlecrystal structure of apo Card1
ComponentsCard1
KeywordsDNA BINDING PROTEIN / Card1 / Dnase / cyclic oligoadenylates
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 / Card1 domain-containing protein
Function and homology information
Biological speciesTreponema succinifaciens
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.32 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.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
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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Card1
B: Card1


Theoretical massNumber of molelcules
Total (without water)90,0262
Polymers90,0262
Non-polymers00
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-9 kcal/mol
Surface area35570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.152, 124.709, 42.643
Angle α, β, γ (deg.)90.000, 96.880, 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: 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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.62 Å3/Da / Density % sol: 53.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.2 M K2HPO4, and 20% PEG3350 (v/v)

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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: 2.32→86.45 Å / Num. obs: 38510 / % possible obs: 98.83 % / Redundancy: 3.9 % / Biso Wilson estimate: 48.72 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.07762 / Rpim(I) all: 0.04496 / Rrim(I) all: 0.09003 / Net I/σ(I): 12.93
Reflection shellResolution: 2.32→2.41 Å / Rmerge(I) obs: 0.7605 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3739 / CC1/2: 0.624 / CC star: 0.877 / Rpim(I) all: 0.4494 / Rrim(I) all: 0.8862

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Processing

Software
NameVersionClassification
PHENIX1.18_3855refinement
XDSdata reduction
XDSdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.32→86.45 Å / SU ML: 0.355 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.0808
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2443 1882 4.9 %
Rwork0.205 36524 -
obs0.207 38406 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.96 Å2
Refinement stepCycle: LAST / Resolution: 2.32→86.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6184 0 0 138 6322
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00676314
X-RAY DIFFRACTIONf_angle_d0.82628514
X-RAY DIFFRACTIONf_chiral_restr0.0575924
X-RAY DIFFRACTIONf_plane_restr0.00451088
X-RAY DIFFRACTIONf_dihedral_angle_d23.09662372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.390.36261450.29792714X-RAY DIFFRACTION95.4
2.39-2.460.33951440.28822778X-RAY DIFFRACTION99.22
2.46-2.540.31591380.27122813X-RAY DIFFRACTION98.89
2.54-2.630.31811430.25422784X-RAY DIFFRACTION98.69
2.63-2.730.33741500.25352788X-RAY DIFFRACTION99.22
2.73-2.860.28131550.24662860X-RAY DIFFRACTION99.34
2.86-3.010.31151390.25042815X-RAY DIFFRACTION99.6
3.01-3.20.30971460.24142790X-RAY DIFFRACTION98.82
3.2-3.440.2771350.21382845X-RAY DIFFRACTION99.53
3.44-3.790.23341510.20062821X-RAY DIFFRACTION99.4
3.79-4.340.20871410.1752827X-RAY DIFFRACTION98.97
4.34-5.470.20041500.15852845X-RAY DIFFRACTION99.4
5.47-86.450.18641450.18322844X-RAY DIFFRACTION98.16

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