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- PDB-7dsy: Crystal Structure of RNase L in complex with KM05073 -

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Basic information

Entry
Database: PDB / ID: 7dsy
TitleCrystal Structure of RNase L in complex with KM05073
ComponentsRibonuclease L
KeywordsHYDROLASE / RNase L / inhibitor / KM05073 / fragment
Function / homology
Function and homology information


RNA nuclease activity / mRNA processing / protein kinase activity / 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 / Chem-HFX / PHOSPHATE ION / Ribonuclease L
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.651 Å
AuthorsTang, J. / Huang, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21778008 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 3, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)165,2597
Polymers162,6562
Non-polymers2,6045
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10050 Å2
ΔGint6 kcal/mol
Surface area58210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.320, 111.050, 262.830
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 567 or (resid 571...

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
21LEULEUGLYGLY(chain b and (resid 23 through 567 or (resid 571...bB23 - 5678 - 552
22GLUGLUGLUGLU(chain b and (resid 23 through 567 or (resid 571...bB571556
23LEULEUTHRTHR(chain b and (resid 23 through 567 or (resid 571...bB23 - 7278 - 712
24LEULEUTHRTHR(chain b and (resid 23 through 567 or (resid 571...bB23 - 7278 - 712
25LEULEUTHRTHR(chain b and (resid 23 through 567 or (resid 571...bB23 - 7278 - 712
26LEULEUTHRTHR(chain b and (resid 23 through 567 or (resid 571...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-HFX / 1-chloranyl-3-methylsulfinyl-6,7-dihydro-5H-2-benzothiophen-4-one


Mass: 248.750 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H9ClO2S2 / 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.: 119 / 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: 2.66 Å3/Da / Density % sol: 53.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG4000, 100 mM Tris, 150 mM (NH4)2SO4, 2mM DTT, 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: 2.65→31.504 Å / Num. obs: 96516 / % possible obs: 99.55 % / Redundancy: 6.5 % / Biso Wilson estimate: 78.76 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06505 / Net I/σ(I): 1.27
Reflection shellResolution: 2.65→2.75 Å / Rmerge(I) obs: 0.9465 / Num. unique obs: 4987

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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: 2.651→31.504 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.15 / Phase error: 32.67 / Stereochemistry target values: ML / Details: the entry contains Friedel pairs
RfactorNum. reflection% reflection
Rfree0.2699 4837 5.01 %
Rwork0.1988 91679 -
obs0.2024 96516 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 236.46 Å2 / Biso mean: 103.5525 Å2 / Biso min: 42.53 Å2
Refinement stepCycle: final / Resolution: 2.651→31.504 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10700 0 167 119 10986
Biso mean--98.38 82.33 -
Num. residues----1348
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11a4084X-RAY DIFFRACTION5.791TORSIONAL
12b4084X-RAY DIFFRACTION5.791TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.651-2.68080.37491540.3674289193
2.6808-2.71230.40191610.34823102100
2.7123-2.74540.46811580.34013014100
2.7454-2.78010.37261640.33243117100
2.7801-2.81670.38961600.3183080100
2.8167-2.85520.40391580.30893117100
2.8552-2.8960.3671590.27893000100
2.896-2.93920.33881620.26663126100
2.9392-2.98510.35111600.25833066100
2.9851-3.0340.35241610.26063026100
3.034-3.08630.27461630.25083109100
3.0863-3.14230.33431670.2533119100
3.1423-3.20270.36271610.25332998100
3.2027-3.2680.36961670.26053091100
3.268-3.3390.35561620.24843082100
3.339-3.41660.30841590.23773047100
3.4166-3.50190.29191640.23013133100
3.5019-3.59650.28411640.21633067100
3.5965-3.70220.33151670.2175310199
3.7022-3.82150.26261560.1941298699
3.8215-3.95780.23351670.1913138100
3.9578-4.11590.31191550.1844296199
4.1159-4.30280.24021570.1738305399
4.3028-4.5290.24191620.1624306699
4.529-4.81190.24051580.1597303599
4.8119-5.18190.2351630.1707301599
5.1819-5.70060.26511650.1801307399
5.7006-6.51910.25881630.1845307799
6.5191-8.18950.20861630.1625302999
8.1895-31.5040.21091570.1608296096
Refinement TLS params.Method: refined / Origin x: 8.8323 Å / Origin y: -26.203 Å / Origin z: -43.2097 Å
111213212223313233
T0.601 Å2-0.0326 Å20.0299 Å2-0.4918 Å20.0244 Å2--0.5736 Å2
L0.6909 °20.2896 °20.3702 °2-1.3329 °20.8211 °2--2.2475 °2
S0.1785 Å °-0.1031 Å °0.0394 Å °0.5574 Å °-0.0148 Å °-0.0987 Å °0.4684 Å °0.2192 Å °-0.1288 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 - 121
8X-RAY DIFFRACTION1allB1

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