[English] 日本語
Yorodumi
- PDB-9lqf: Crystal structure of SAM lyase in complex with SAH-AMP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9lqf
TitleCrystal structure of SAM lyase in complex with SAH-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: 1.59 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SAM lyase
D: SAM lyase
E: SAM lyase
B: SAM lyase
C: 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)181,21033
Polymers171,81812
Non-polymers9,39221
Water23,2391290
1
A: SAM lyase
D: SAM lyase
E: SAM lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2798
Polymers42,9543
Non-polymers2,3255
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9050 Å2
ΔGint-31 kcal/mol
Surface area15270 Å2
MethodPISA
2
B: SAM lyase
C: SAM lyase
F: SAM lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3729
Polymers42,9543
Non-polymers2,4176
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9190 Å2
ΔGint-35 kcal/mol
Surface area15310 Å2
MethodPISA
3
G: SAM lyase
H: SAM lyase
I: SAM lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2798
Polymers42,9543
Non-polymers2,3255
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9030 Å2
ΔGint-34 kcal/mol
Surface area15320 Å2
MethodPISA
4
J: SAM lyase
K: SAM lyase
L: SAM lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2798
Polymers42,9543
Non-polymers2,3255
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9130 Å2
ΔGint-34 kcal/mol
Surface area15210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.940, 109.930, 94.220
Angle α, β, γ (deg.)90.00, 111.07, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
SAM lyase


Mass: 14318.152 Da / Num. of mol.: 12
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-A1EL0 / (2~{S})-4-[[(2~{S},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]methylsulfanyl]-2-azanyl-butanoic acid


Mass: 713.617 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C24H32N11O11PS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1290 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium sulfate, 20% w/v Polyethylene glycol 3,350

-
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: 1.59→69.68 Å / Num. obs: 195466 / % possible obs: 98.6 % / Redundancy: 6 % / CC1/2: 0.998 / Net I/σ(I): 10.2
Reflection shellResolution: 1.59→1.63 Å / Num. unique obs: 14070 / CC1/2: 0.409

-
Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
XDSdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.59→45.57 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2229 9792 5.01 %
Rwork0.1865 --
obs0.1884 195402 98.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.59→45.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11928 0 630 1290 13848
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d0.991
X-RAY DIFFRACTIONf_dihedral_angle_d21.1454808
X-RAY DIFFRACTIONf_chiral_restr0.0591932
X-RAY DIFFRACTIONf_plane_restr0.0042116
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.610.35712910.3345930X-RAY DIFFRACTION95
1.61-1.630.33343300.31766076X-RAY DIFFRACTION97
1.63-1.650.32263090.30776100X-RAY DIFFRACTION97
1.65-1.670.30743220.2816071X-RAY DIFFRACTION97
1.67-1.690.31333290.26156111X-RAY DIFFRACTION97
1.69-1.710.28822540.25436155X-RAY DIFFRACTION98
1.71-1.740.29253090.24866132X-RAY DIFFRACTION98
1.74-1.760.30643080.23896195X-RAY DIFFRACTION99
1.76-1.790.28373090.23436211X-RAY DIFFRACTION99
1.79-1.820.25873150.22156245X-RAY DIFFRACTION99
1.82-1.850.26983340.21256173X-RAY DIFFRACTION98
1.85-1.890.26723270.21086135X-RAY DIFFRACTION99
1.89-1.920.25753190.21446214X-RAY DIFFRACTION99
1.92-1.960.25063300.21456169X-RAY DIFFRACTION98
1.96-20.25562990.19966261X-RAY DIFFRACTION99
2-2.050.24693060.19636227X-RAY DIFFRACTION99
2.05-2.10.26323320.20166136X-RAY DIFFRACTION99
2.1-2.160.25313300.18886189X-RAY DIFFRACTION99
2.16-2.220.22983380.18546252X-RAY DIFFRACTION99
2.22-2.290.20793390.18016243X-RAY DIFFRACTION99
2.29-2.380.2263490.18016186X-RAY DIFFRACTION100
2.38-2.470.22243370.1816225X-RAY DIFFRACTION99
2.47-2.580.21643160.16926317X-RAY DIFFRACTION100
2.58-2.720.2073350.17826221X-RAY DIFFRACTION100
2.72-2.890.22473960.17796252X-RAY DIFFRACTION100
2.89-3.110.21943590.17656212X-RAY DIFFRACTION100
3.11-3.430.18733450.16166239X-RAY DIFFRACTION99
3.43-3.920.21033700.15716251X-RAY DIFFRACTION99
3.92-4.940.15723560.1376258X-RAY DIFFRACTION99
4.94-45.570.16852990.15916224X-RAY DIFFRACTION97

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more