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- PDB-7dts: Crystal structure of RNase L in complex with AC40357 -

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Basic information

Entry
Database: PDB / ID: 7dts
TitleCrystal structure of RNase L in complex with AC40357
ComponentsRibonuclease L
KeywordsHYDROLASE / RNase L / Fragment / inhibitor
Function / homology
Function and homology information


regulation of RNA metabolic process / negative regulation of viral genome replication / RNA nuclease activity / mRNA processing / defense response to virus / protein kinase activity / RNA binding / ATP binding / metal ion binding
Similarity search - Function
RNase L, RNase domain / KEN domain / KEN domain superfamily / Ribonuclease 2-5A / KEN domain profile. / domain in protein kinases, N-glycanases and other nuclear proteins / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. ...RNase L, RNase domain / KEN domain / KEN domain superfamily / Ribonuclease 2-5A / KEN domain profile. / domain in protein kinases, N-glycanases and other nuclear proteins / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-25A / butyl 4-hydroxybenzoate / PHOSPHATE ION / Ribonuclease L
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å
AuthorsTang, J. / Huang, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21778808 China
CitationJournal: J.Med.Chem. / Year: 2022
Title: Identification of Small Molecule Inhibitors of RNase L by Fragment-Based Drug Discovery
Authors: Tang, J. / Dong, B. / Liu, M. / Liu, S. / Niu, X. / Gaughan, C. / Asthana, A. / Zhou, H. / Xu, Z. / Zhang, G. / Silverman, R.H. / Huang, H.
History
DepositionJan 6, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2022Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
a: Ribonuclease L
b: Ribonuclease L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,1507
Polymers162,6562
Non-polymers2,4955
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9730 Å2
ΔGint1 kcal/mol
Surface area59680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.010, 111.280, 264.090
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain a and ((resid 23 and (name N or name...
21(chain b and (resid 23 through 321 or resid 333...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEULEULEU(chain a and ((resid 23 and (name N or name...aA238
12SERSERTHRTHR(chain a and ((resid 23 and (name N or name...aA22 - 7277 - 712
13SERSERTHRTHR(chain a and ((resid 23 and (name N or name...aA22 - 7277 - 712
14SERSERTHRTHR(chain a and ((resid 23 and (name N or name...aA22 - 7277 - 712
15SERSERTHRTHR(chain a and ((resid 23 and (name N or name...aA22 - 7277 - 712
16SERSERTHRTHR(chain a and ((resid 23 and (name N or name...aA22 - 7277 - 712
21LEULEUHISHIS(chain b and (resid 23 through 321 or resid 333...bB23 - 3218 - 306
22ASNASNALAALA(chain b and (resid 23 through 321 or resid 333...bB333 - 373318 - 358
23GLUGLUGLUGLU(chain b and (resid 23 through 321 or resid 333...bB374359
24LEULEUTHRTHR(chain b and (resid 23 through 321 or resid 333...bB23 - 7278 - 712
25LEULEUTHRTHR(chain b and (resid 23 through 321 or resid 333...bB23 - 7278 - 712
26LEULEUTHRTHR(chain b and (resid 23 through 321 or resid 333...bB23 - 7278 - 712
27LEULEUTHRTHR(chain b and (resid 23 through 321 or resid 333...bB23 - 7278 - 712
28LEULEUTHRTHR(chain b and (resid 23 through 321 or resid 333...bB23 - 7278 - 712
29LEULEUTHRTHR(chain b and (resid 23 through 321 or resid 333...bB23 - 7278 - 712
210LEULEUTHRTHR(chain b and (resid 23 through 321 or resid 333...bB23 - 7278 - 712

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Components

#1: Protein Ribonuclease L


Mass: 81327.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: RNASEL / Production host: Escherichia coli (E. coli) / References: UniProt: A5H025
#2: Chemical ChemComp-25A / 5'-O-MONOPHOSPHORYLADENYLYL(2'->5')ADENYLYL(2'->5')ADENOSINE


Mass: 1005.633 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H38N15O19P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-27K / butyl 4-hydroxybenzoate


Mass: 194.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H14O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.67 Å3/Da / Density % sol: 53.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG4000, 100 mM Tris, 150 mM (NH4)2SO4 and 2 mM DTT buffer, pH 7.5
PH range: 7.0 - 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.63→30.55 Å / Num. obs: 52595 / % possible obs: 99.52 % / Redundancy: 6.3 % / Biso Wilson estimate: 79.3 Å2 / CC1/2: 0.999 / Net I/σ(I): 1.45
Reflection shellResolution: 2.63→2.73 Å / Rmerge(I) obs: 1.297 / Num. unique obs: 5182

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M11

6m11


Resolution: 2.63→30.355 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2703 2700 5.14 %
Rwork0.1917 49855 -
obs0.1957 52555 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 222.14 Å2 / Biso mean: 99.3852 Å2 / Biso min: 42.7 Å2
Refinement stepCycle: final / Resolution: 2.63→30.355 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10727 0 167 98 10992
Biso mean--92.5 84.35 -
Num. residues----1352
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11a4076X-RAY DIFFRACTION5.928TORSIONAL
12b4076X-RAY DIFFRACTION5.928TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.63-2.67780.32311480.26822619100
2.6778-2.72930.35821370.27792546100
2.7293-2.7850.38551620.2832602100
2.785-2.84550.34771300.28092581100
2.8455-2.91160.35081590.27272541100
2.9116-2.98440.41041350.26192632100
2.9844-3.0650.34951210.26162613100
3.065-3.15510.35081300.25532609100
3.1551-3.25680.32891390.24562615100
3.2568-3.37310.35341300.22762619100
3.3731-3.5080.28821480.21752610100
3.508-3.66730.28421310.21142630100
3.6673-3.86030.25021230.19532624100
3.8603-4.10170.3091170.1905262299
4.1017-4.41750.24711670.1807261999
4.4175-4.86040.23721610.16222657100
4.8604-5.560.2721690.1711262699
5.56-6.99080.26781410.1892271199
6.9908-30.3550.20381520.1429277998
Refinement TLS params.Method: refined / Origin x: 8.9648 Å / Origin y: -25.8343 Å / Origin z: -43.3066 Å
111213212223313233
T0.5358 Å2-0.0582 Å20.0093 Å2-0.5274 Å2-0.0128 Å2--0.6646 Å2
L0.5345 °20.2348 °20.1456 °2-0.9775 °20.4371 °2--1.5887 °2
S0.1256 Å °-0.0723 Å °0.1155 Å °0.4495 Å °-0.0345 Å °-0.027 Å °0.2392 Å °0.2189 Å °-0.0848 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1alla22 - 727
2X-RAY DIFFRACTION1alla801
3X-RAY DIFFRACTION1alla901
4X-RAY DIFFRACTION1allb23 - 727
5X-RAY DIFFRACTION1allb801
6X-RAY DIFFRACTION1allb901
7X-RAY DIFFRACTION1allA1 - 98
8X-RAY DIFFRACTION1allB1

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