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- PDB-8t66: cA6 bound Cam1 -

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Basic information

Entry
Database: PDB / ID: 8t66
TitlecA6 bound Cam1
Components
  • Cam1
  • RNA (5'-R(P*AP*AP*AP*AP*A)-3')
KeywordsIMMUNE SYSTEM/RNA / CARF / SAVED / Membrane / CRISPR / Cyclic adenylate / IMMUNE SYSTEM / IMMUNE SYSTEM-RNA complex
Function / homologymembrane / RNA / Uncharacterized protein
Function and homology information
Biological speciesNitrosococcus halophilus Nc 4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsYu, Y. / Patel, D.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)GM129430 United States
CitationJournal: Nature / Year: 2024
Title: The CRISPR effector Cam1 mediates membrane depolarization for phage defence.
Authors: Baca, C.F. / Yu, Y. / Rostol, J.T. / Majumder, P. / Patel, D.J. / Marraffini, L.A.
History
DepositionJun 15, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 7, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Cam1
A: Cam1
C: RNA (5'-R(P*AP*AP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)37,7953
Polymers37,7953
Non-polymers00
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-18 kcal/mol
Surface area13210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.352, 75.813, 125.195
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Cam1


Mass: 17932.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitrosococcus halophilus Nc 4 (bacteria)
Strain: Nc4 / Gene: Nhal_2839 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D5BXZ3
#2: RNA chain RNA (5'-R(P*AP*AP*AP*AP*A)-3')


Mass: 1930.277 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Nitrosococcus halophilus Nc 4 (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.21 Å3/Da / Density % sol: 44.3 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.05 M Magnesium Chloride hexahydrate, 0.1 M HEPES, pH 7.5, 30% (w/v) PEGMME 550

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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 EIGER X 16M / Detector: PIXEL / Date: Jul 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.85→125.2 Å / Num. obs: 28724 / % possible obs: 99.1 % / Redundancy: 8.7 % / Biso Wilson estimate: 25.23 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.214 / Net I/σ(I): 19.4
Reflection shellResolution: 1.85→1.89 Å / Rmerge(I) obs: 1.01 / Num. unique obs: 1488 / CC1/2: 0.784 / Rpim(I) all: 0.39

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→62.6 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2222 1331 4.65 %
Rwork0.1956 --
obs0.1969 28616 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→62.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2316 110 0 166 2592
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082489
X-RAY DIFFRACTIONf_angle_d0.9473405
X-RAY DIFFRACTIONf_dihedral_angle_d23.864926
X-RAY DIFFRACTIONf_chiral_restr0.063398
X-RAY DIFFRACTIONf_plane_restr0.006430
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.920.32671310.33382433X-RAY DIFFRACTION90
1.92-1.990.25451260.22062734X-RAY DIFFRACTION100
1.99-2.080.21191100.1842728X-RAY DIFFRACTION100
2.08-2.190.23221420.1862702X-RAY DIFFRACTION100
2.19-2.330.22881520.17912724X-RAY DIFFRACTION100
2.33-2.510.21691280.18532738X-RAY DIFFRACTION100
2.51-2.760.2334980.18762793X-RAY DIFFRACTION100
2.76-3.160.21481360.19482765X-RAY DIFFRACTION100
3.16-3.990.19971550.18982791X-RAY DIFFRACTION100
3.99-62.60.2231530.19832877X-RAY DIFFRACTION100

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