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- PDB-9lqh: Crystal structure of SAM lyase in complex with sinefungin-AMP -

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Basic information

Entry
Database: PDB / ID: 9lqh
TitleCrystal structure of SAM lyase in complex with sinefungin-AMP
ComponentsSAM lyase
KeywordsIMMUNE SYSTEM / enzyme / SAM / CRISPR-Cas system / second messenger
Function / homology: / Uncharacterized protein
Function and homology information
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsDuan, B. / Zhao, B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Mechanisms of SAM-AMP synthesis and degradation in antiviral type III CRISPR signaling.
Authors: Duan, B. / Zhao, B.
History
DepositionJan 28, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SAM lyase
B: SAM lyase
C: SAM lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0866
Polymers42,9543
Non-polymers2,1323
Water7,170398
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8320 Å2
ΔGint-33 kcal/mol
Surface area15480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.160, 53.880, 153.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SAM lyase


Mass: 14318.152 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: deletions
Source: (gene. exp.) Clostridium botulinum (strain Hall / ATCC 3502 / NCTC 13319 / Type A) (bacteria)
Gene: CBO2178 / Production host: Escherichia coli (E. coli) / References: UniProt: A5I3U9
#2: Chemical ChemComp-A1EL1 / (2~{S},5~{S})-6-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-4-oxidanyl-oxolan-2-yl]-2,5-bis(azanyl)hexanoic acid


Mass: 710.593 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C25H35N12O11P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.27 Å3/Da / Density % sol: 45.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 0.1 M Sodium acetate trihydrate pH 4.0, 15% v/v Polyethylene glycol 400

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Data collection

DiffractionMean temperature: 153 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 20, 2024
RadiationMonochromator: Si(111) DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.47→51.12 Å / Num. obs: 66545 / % possible obs: 98.8 % / Redundancy: 10.6 % / CC1/2: 0.997 / Net I/σ(I): 16.6
Reflection shellResolution: 1.47→1.51 Å / Num. unique obs: 4681 / CC1/2: 0.666

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
XDSdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.47→22.54 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2174 3294 4.96 %
Rwork0.1882 --
obs0.1896 66429 98.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.47→22.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2990 0 147 398 3535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d1.045
X-RAY DIFFRACTIONf_dihedral_angle_d21.131194
X-RAY DIFFRACTIONf_chiral_restr0.079485
X-RAY DIFFRACTIONf_plane_restr0.004527
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.47-1.490.31421440.29172442X-RAY DIFFRACTION94
1.49-1.510.34531250.28992541X-RAY DIFFRACTION97
1.51-1.540.38851410.33172442X-RAY DIFFRACTION93
1.54-1.560.25781410.23592589X-RAY DIFFRACTION98
1.56-1.590.2451220.21762604X-RAY DIFFRACTION98
1.59-1.620.23261260.20282578X-RAY DIFFRACTION98
1.62-1.650.2421450.19752597X-RAY DIFFRACTION99
1.65-1.680.21351510.19492622X-RAY DIFFRACTION99
1.68-1.720.20281390.19572585X-RAY DIFFRACTION99
1.72-1.760.21281090.1942632X-RAY DIFFRACTION99
1.76-1.80.18871470.18722656X-RAY DIFFRACTION100
1.8-1.850.24191370.18932608X-RAY DIFFRACTION99
1.85-1.910.19581190.19872656X-RAY DIFFRACTION99
1.91-1.970.24951300.2212615X-RAY DIFFRACTION98
1.97-2.040.24221290.17872664X-RAY DIFFRACTION100
2.04-2.120.23731440.20642607X-RAY DIFFRACTION98
2.12-2.220.20671250.1862666X-RAY DIFFRACTION100
2.22-2.330.22131360.19382661X-RAY DIFFRACTION99
2.33-2.480.19151410.18972692X-RAY DIFFRACTION100
2.48-2.670.23021430.1862663X-RAY DIFFRACTION100
2.67-2.940.22761420.18142703X-RAY DIFFRACTION100
2.94-3.360.19731600.16532715X-RAY DIFFRACTION100
3.36-4.230.16961440.1572725X-RAY DIFFRACTION99
4.23-22.540.18441540.14712872X-RAY DIFFRACTION99

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