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- PDB-9lqe: Crystal structure of SAM lyase in complex with SAH -

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Basic information

Entry
Database: PDB / ID: 9lqe
TitleCrystal structure of SAM lyase in complex with SAH
ComponentsSAM lyase
KeywordsIMMUNE SYSTEM / enzyme / SAM / CRISPR-Cas system / second messenger
Function / homologyS-ADENOSYL-L-HOMOCYSTEINE / Uncharacterized protein
Function and homology information
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 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

Downloads & links

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Assembly

Deposited unit
A: SAM lyase
B: SAM lyase
C: SAM lyase
D: SAM lyase
E: SAM lyase
F: SAM lyase
G: SAM lyase
H: SAM lyase
I: SAM lyase
J: SAM lyase
K: SAM lyase
L: SAM lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,27534
Polymers171,81812
Non-polymers8,45722
Water16,484915
1
A: SAM lyase
B: SAM lyase
C: SAM lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2619
Polymers42,9543
Non-polymers2,3066
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8150 Å2
ΔGint-23 kcal/mol
Surface area15410 Å2
MethodPISA
2
D: SAM lyase
E: SAM lyase
F: SAM lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2619
Polymers42,9543
Non-polymers2,3066
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8090 Å2
ΔGint-23 kcal/mol
Surface area15330 Å2
MethodPISA
3
G: SAM lyase
H: SAM lyase
I: SAM lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8778
Polymers42,9543
Non-polymers1,9225
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7900 Å2
ΔGint-24 kcal/mol
Surface area15650 Å2
MethodPISA
4
J: SAM lyase
K: SAM lyase
L: SAM lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8778
Polymers42,9543
Non-polymers1,9225
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7920 Å2
ΔGint-25 kcal/mol
Surface area15440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.588, 124.588, 138.564
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein
SAM lyase


Mass: 14318.152 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
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-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 915 / 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: 3.13 Å3/Da / Density % sol: 60.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 30% w/v Polyethylene glycol 1,000

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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: 1.94→88.1 Å / Num. obs: 155895 / % possible obs: 100 % / Redundancy: 12.7 % / CC1/2: 0.998 / Net I/σ(I): 8
Reflection shellResolution: 1.94→1.99 Å / Num. unique obs: 11501 / CC1/2: 0.673

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
xia2data scaling
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→88.1 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2185 7725 4.97 %
Rwork0.1853 --
obs0.1869 155277 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.94→88.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11978 0 572 915 13465
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.793
X-RAY DIFFRACTIONf_dihedral_angle_d18.6514567
X-RAY DIFFRACTIONf_chiral_restr0.0521936
X-RAY DIFFRACTIONf_plane_restr0.0042127
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.960.30632480.2674792X-RAY DIFFRACTION97
1.96-1.980.30162520.24134921X-RAY DIFFRACTION100
1.98-2.010.25272590.22744961X-RAY DIFFRACTION100
2.01-2.030.25642560.21834915X-RAY DIFFRACTION100
2.03-2.060.24032760.2114849X-RAY DIFFRACTION100
2.06-2.090.22582650.20274906X-RAY DIFFRACTION100
2.09-2.120.22492960.20444901X-RAY DIFFRACTION100
2.12-2.150.27232140.20524942X-RAY DIFFRACTION100
2.15-2.180.24782770.20814892X-RAY DIFFRACTION100
2.18-2.220.25222570.22344896X-RAY DIFFRACTION99
2.22-2.260.27452520.22824897X-RAY DIFFRACTION99
2.26-2.30.28872840.22754870X-RAY DIFFRACTION99
2.3-2.340.26152270.23144910X-RAY DIFFRACTION99
2.34-2.390.28772550.23254927X-RAY DIFFRACTION99
2.39-2.440.26332570.22214932X-RAY DIFFRACTION100
2.44-2.50.26882250.21024885X-RAY DIFFRACTION99
2.5-2.560.27052600.21014903X-RAY DIFFRACTION100
2.56-2.630.23512470.2024944X-RAY DIFFRACTION100
2.63-2.710.27412570.20574931X-RAY DIFFRACTION100
2.71-2.80.24332430.214908X-RAY DIFFRACTION100
2.8-2.90.20792490.20374938X-RAY DIFFRACTION100
2.9-3.010.22932610.20014916X-RAY DIFFRACTION99
3.01-3.150.23792510.1974942X-RAY DIFFRACTION100
3.15-3.320.21212760.17764931X-RAY DIFFRACTION100
3.32-3.520.21412950.1794896X-RAY DIFFRACTION100
3.52-3.80.2242510.16474965X-RAY DIFFRACTION100
3.8-4.180.18352480.15584954X-RAY DIFFRACTION100
4.18-4.780.14522650.13874973X-RAY DIFFRACTION100
4.78-6.030.18572680.15414965X-RAY DIFFRACTION100
6.03-88.10.15732540.14554990X-RAY DIFFRACTION99

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