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- PDB-8t64: Apo Cam1(42-206) -

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Basic information

Entry
Database: PDB / ID: 8t64
TitleApo Cam1(42-206)
ComponentsCam1
KeywordsIMMUNE SYSTEM / CARF / SAVED / Membrane / CRISPR / Cyclic adenylate
Function / homologymembrane / Uncharacterized protein
Function and homology information
Biological speciesNitrosococcus halophilus Nc 4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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
A: Cam1
B: Cam1
C: Cam1
D: Cam1


Theoretical massNumber of molelcules
Total (without water)71,7304
Polymers71,7304
Non-polymers00
Water1,76598
1
A: Cam1
B: Cam1


Theoretical massNumber of molelcules
Total (without water)35,8652
Polymers35,8652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-32 kcal/mol
Surface area11060 Å2
MethodPISA
2
C: Cam1
D: Cam1


Theoretical massNumber of molelcules
Total (without water)35,8652
Polymers35,8652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-37 kcal/mol
Surface area11970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.783, 120.551, 51.544
Angle α, β, γ (deg.)90.00, 115.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Cam1


Mass: 17932.430 Da / Num. of mol.: 4
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 1.71 Å3/Da / Density % sol: 28.23 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium chloride, 0.1 M sodium cacodylate trihydrate, pH 6.6, 25% PEG3350 (w/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 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: 2.25→50 Å / Num. obs: 96801 / % possible obs: 97.8 % / Redundancy: 4.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.083 / Net I/σ(I): 24.3
Reflection shellResolution: 2.25→2.33 Å / Num. unique obs: 22371 / CC1/2: 0.955

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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: 2.25→46.59 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 26.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2441 1058 4.74 %
Rwork0.2053 --
obs0.2071 22333 97.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→46.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3904 0 0 98 4002
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0163981
X-RAY DIFFRACTIONf_angle_d1.2815421
X-RAY DIFFRACTIONf_dihedral_angle_d25.0411433
X-RAY DIFFRACTIONf_chiral_restr0.076646
X-RAY DIFFRACTIONf_plane_restr0.007708
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.350.31331300.25842601X-RAY DIFFRACTION96
2.35-2.480.28111370.24152690X-RAY DIFFRACTION99
2.48-2.630.31051640.23782636X-RAY DIFFRACTION99
2.63-2.840.24281200.24152732X-RAY DIFFRACTION99
2.84-3.120.29861250.24092686X-RAY DIFFRACTION99
3.12-3.570.25851370.20642684X-RAY DIFFRACTION99
3.58-4.50.23381080.17842617X-RAY DIFFRACTION95
4.5-46.590.18321370.1772629X-RAY DIFFRACTION95

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