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- PDB-8kbj: Structure of HgmTad2 complexed with 1',2'-cADPR -

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Basic information

Entry
Database: PDB / ID: 8kbj
TitleStructure of HgmTad2 complexed with 1',2'-cADPR
ComponentsInhibitor of Type II CRISPR-Cas system
KeywordsVIRAL PROTEIN
Function / homologyProtein of unknown function DUF2829 / Protein of unknown function (DUF2829) / Chem-MF6 / Inhibitor of Type II CRISPR-Cas system
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsXiao, Y. / Feng, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nature / Year: 2024
Title: Single phage proteins sequester signals from TIR and cGAS-like enzymes.
Authors: Li, D. / Xiao, Y. / Fedorova, I. / Xiong, W. / Wang, Y. / Liu, X. / Huiting, E. / Ren, J. / Gao, Z. / Zhao, X. / Cao, X. / Zhang, Y. / Bondy-Denomy, J. / Feng, Y.
History
DepositionAug 4, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2024Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.3Nov 6, 2024Group: 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 1.4Nov 13, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inhibitor of Type II CRISPR-Cas system
C: Inhibitor of Type II CRISPR-Cas system
D: Inhibitor of Type II CRISPR-Cas system
B: Inhibitor of Type II CRISPR-Cas system
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6917
Polymers48,0674
Non-polymers1,6243
Water3,261181
1
A: Inhibitor of Type II CRISPR-Cas system
hetero molecules

B: Inhibitor of Type II CRISPR-Cas system


Theoretical massNumber of molelcules
Total (without water)24,5753
Polymers24,0342
Non-polymers5411
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
2
C: Inhibitor of Type II CRISPR-Cas system
D: Inhibitor of Type II CRISPR-Cas system
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1164
Polymers24,0342
Non-polymers1,0832
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.812, 101.812, 92.305
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11C-201-

MF6

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Components

#1: Protein
Inhibitor of Type II CRISPR-Cas system


Mass: 12016.822 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Gene: acrIIA7 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A447EB45
#2: Chemical ChemComp-MF6 / (1S,3R,4R,6R,9S,11R,14R,15S,16R,18R)-4-(6-amino-9H-purin-9-yl)-9,11,15,16,18-pentahydroxy-2,5,8,10,12,17-hexaoxa-9lambda~5~,11lambda~5~-diphosphatricyclo[12.2.1.1~3,6~]octadecane-9,11-dione / 1'-2' gcADPR


Mass: 541.300 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H21N5O13P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.51 Å3/Da / Density % sol: 51.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Potassium thiocyanate, 20% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: May 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→45.56 Å / Num. obs: 29066 / % possible obs: 100 % / Redundancy: 25.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.234 / Rpim(I) all: 0.047 / Rrim(I) all: 0.239 / Χ2: 0.96 / Net I/σ(I): 15.7 / Num. measured all: 736493
Reflection shellResolution: 2.1→2.15 Å / % possible obs: 100 % / Redundancy: 24.8 % / Rmerge(I) obs: 2.055 / Num. measured all: 52755 / Num. unique obs: 2131 / CC1/2: 0.978 / Rpim(I) all: 0.42 / Rrim(I) all: 2.098 / Χ2: 0.89 / Net I/σ(I) obs: 5.8

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→45.53 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.236 1506 5.19 %
Rwork0.192 --
obs0.1942 29009 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→45.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3254 0 105 181 3540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0183516
X-RAY DIFFRACTIONf_angle_d2.3084780
X-RAY DIFFRACTIONf_dihedral_angle_d26.334524
X-RAY DIFFRACTIONf_chiral_restr0.096520
X-RAY DIFFRACTIONf_plane_restr0.027584
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.160.24451330.18952403X-RAY DIFFRACTION98
2.16-2.240.26781500.19672423X-RAY DIFFRACTION100
2.24-2.330.26111450.19472461X-RAY DIFFRACTION100
2.33-2.440.23991550.19192460X-RAY DIFFRACTION100
2.44-2.570.23111380.19422465X-RAY DIFFRACTION100
2.57-2.730.24351230.19492489X-RAY DIFFRACTION100
2.73-2.940.26571180.20622504X-RAY DIFFRACTION100
2.94-3.230.26381200.19282514X-RAY DIFFRACTION100
3.23-3.70.22671540.18382514X-RAY DIFFRACTION100
3.7-4.660.21981280.17032566X-RAY DIFFRACTION100
4.66-45.530.21331420.21172704X-RAY DIFFRACTION100

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