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- PDB-6xl1: crystal structure of cA4-activated Card1(D294N) -

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Basic information

Entry
Database: PDB / ID: 6xl1
Titlecrystal structure of cA4-activated Card1(D294N)
Components
  • Card1
  • cA4
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 DSM 2489 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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
DepositionJun 27, 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 / struct
Item: _citation.title / _entity.pdbx_description ..._citation.title / _entity.pdbx_description / _struct.pdbx_descriptor / _struct.title
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 1.5Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Card1
B: Card1
C: cA4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,7548
Polymers91,2963
Non-polymers4585
Water9,944552
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6300 Å2
ΔGint-29 kcal/mol
Surface area33070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.946, 111.946, 172.180
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Card1


Mass: 45012.059 Da / Num. of mol.: 2 / Mutation: D294N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema succinifaciens DSM 2489 (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.: 1 / 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
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 552 / Source method: isolated from a natural source / Formula: H2O
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: 2.95 Å3/Da / Density % sol: 58.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M HEPES 7.0, 30% (v/v) Jeffamine M-600

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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: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.95→40 Å / Num. obs: 80132 / % possible obs: 99.91 % / Redundancy: 15 % / Biso Wilson estimate: 31.61 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.08062 / Rpim(I) all: 0.02133 / Rrim(I) all: 0.08345 / Net I/σ(I): 23.41
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 15.2 % / Rmerge(I) obs: 0.661 / Mean I/σ(I) obs: 4.08 / Num. unique obs: 7872 / CC1/2: 0.936 / CC star: 0.983 / Rpim(I) all: 0.1742 / Rrim(I) all: 0.684 / % possible all: 99.94

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Processing

Software
NameVersionClassification
PHENIX1.18_3855refinement
PHENIX1.18_3855refinement
autoXDSdata reduction
autoXDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6wwx

6wwx


Resolution: 1.95→39.58 Å / SU ML: 0.1693 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.3025
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2016 4033 5.03 %
Rwork0.1779 76088 -
obs0.1791 80121 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.81 Å2
Refinement stepCycle: LAST / Resolution: 1.95→39.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6200 88 19 552 6859
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00786444
X-RAY DIFFRACTIONf_angle_d0.84288706
X-RAY DIFFRACTIONf_chiral_restr0.0605946
X-RAY DIFFRACTIONf_plane_restr0.00451094
X-RAY DIFFRACTIONf_dihedral_angle_d24.39172435
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.970.20671510.19112569X-RAY DIFFRACTION99.85
1.97-20.23841130.18942630X-RAY DIFFRACTION100
2-2.020.23711420.18712532X-RAY DIFFRACTION99.96
2.02-2.050.22681320.19412618X-RAY DIFFRACTION100
2.05-2.080.24241290.19092607X-RAY DIFFRACTION100
2.08-2.110.22781470.19822571X-RAY DIFFRACTION100
2.11-2.140.24521250.19042600X-RAY DIFFRACTION99.96
2.14-2.170.22811400.18012573X-RAY DIFFRACTION99.93
2.17-2.210.2031420.17742611X-RAY DIFFRACTION100
2.21-2.250.23331330.18532537X-RAY DIFFRACTION98.93
2.25-2.290.20221290.18982628X-RAY DIFFRACTION100
2.29-2.330.21481390.18752596X-RAY DIFFRACTION100
2.33-2.380.21871360.1922574X-RAY DIFFRACTION100
2.38-2.430.24791460.19712623X-RAY DIFFRACTION100
2.43-2.490.24981250.20022611X-RAY DIFFRACTION99.96
2.49-2.550.21031300.19472635X-RAY DIFFRACTION100
2.55-2.620.23841480.1982573X-RAY DIFFRACTION100
2.62-2.690.22521610.22601X-RAY DIFFRACTION100
2.69-2.780.221410.20112613X-RAY DIFFRACTION99.96
2.78-2.880.22071680.19122601X-RAY DIFFRACTION100
2.88-30.25561420.2022600X-RAY DIFFRACTION100
3-3.130.2111320.18792654X-RAY DIFFRACTION100
3.13-3.30.21521160.18012667X-RAY DIFFRACTION99.68
3.3-3.50.19261460.17122628X-RAY DIFFRACTION100
3.5-3.770.1661490.16782655X-RAY DIFFRACTION100
3.77-4.150.17371380.15842671X-RAY DIFFRACTION100
4.15-4.750.15151180.14142713X-RAY DIFFRACTION100
4.75-5.980.18251500.17212721X-RAY DIFFRACTION99.97
5.98-39.580.18571650.17292876X-RAY DIFFRACTION99.9

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