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- PDB-6ls1: Ribonuclease from Hericium erinaceus active and GMP binding form -

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Basic information

Entry
Database: PDB / ID: 6ls1
TitleRibonuclease from Hericium erinaceus active and GMP binding form
ComponentsRibonuclease T1
KeywordsRNA BINDING PROTEIN / RNA Binding Endoribonuclease Activity Ribonuclease Activity
Function / homology
Function and homology information


RNA endonuclease activity / lyase activity / RNA binding / metal ion binding
Similarity search - Function
: / : / Guanine-specific ribonuclease N1/T1/U2 / Ribonuclease/ribotoxin / ribonuclease
Similarity search - Domain/homology
GUANOSINE / DI(HYDROXYETHYL)ETHER / Ribonuclease T1
Similarity search - Component
Biological speciesHericium erinaceus (lion's mane mushroom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.58 Å
AuthorsTakebe, K. / Suzuki, M. / Sangawa, T. / Kobayashi, H. / Itagaki, T.
CitationJournal: To Be Published
Title: Ribonuclease from Hericium erinaceus active and GMP binding form
Authors: Takebe, K. / Suzuki, M. / Sangawa, T. / Kobayashi, H.
History
DepositionJan 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease T1
B: Ribonuclease T1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9165
Polymers21,4312
Non-polymers4853
Water3,675204
1
A: Ribonuclease T1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1053
Polymers10,7151
Non-polymers3892
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5260 Å2
MethodPISA
2
B: Ribonuclease T1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8112
Polymers10,7151
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-16 kcal/mol
Surface area5260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.760, 97.760, 68.910
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 4 or resid 7...
21(chain B and (resid 2 through 4 or resid 7...

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
11SERSERGLYGLY(chain A and (resid 2 through 4 or resid 7...AA2 - 42 - 4
12CYSCYSARGARG(chain A and (resid 2 through 4 or resid 7...AA7 - 107 - 10
13TYRTYRSERSER(chain A and (resid 2 through 4 or resid 7...AA12 - 1312 - 13
14GLNGLNPHEPHE(chain A and (resid 2 through 4 or resid 7...AA1 - 1001 - 100
15GLYGLYCYSCYS(chain A and (resid 2 through 4 or resid 7...AA94 - 9894 - 98
16GLYGLYCYSCYS(chain A and (resid 2 through 4 or resid 7...AA94 - 9894 - 98
17PHEPHEPHEPHE(chain A and (resid 2 through 4 or resid 7...AA100100
21SERSERGLYGLY(chain B and (resid 2 through 4 or resid 7...BB2 - 42 - 4
22CYSCYSARGARG(chain B and (resid 2 through 4 or resid 7...BB7 - 107 - 10
23TYRTYRSERSER(chain B and (resid 2 through 4 or resid 7...BB12 - 1312 - 13
24SERSERGLYGLY(chain B and (resid 2 through 4 or resid 7...BB15 - 2615 - 26
25GLNGLNPHEPHE(chain B and (resid 2 through 4 or resid 7...BB1 - 1001 - 100
26GLYGLYCYSCYS(chain B and (resid 2 through 4 or resid 7...BB94 - 9894 - 98
27GLYGLYCYSCYS(chain B and (resid 2 through 4 or resid 7...BB94 - 9894 - 98
28PHEPHEPHEPHE(chain B and (resid 2 through 4 or resid 7...BB100100

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Components

#1: Protein Ribonuclease T1


Mass: 10715.292 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hericium erinaceus (lion's mane mushroom)
Gene: RNHe1 / Production host: Escherichia coli (E. coli) / References: UniProt: B1Q4V2
#2: Chemical ChemComp-GMP / GUANOSINE


Mass: 283.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 1.92 Å3/Da / Density % sol: 35.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.4M Magnesium sulfate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.58→48.88 Å / Num. obs: 23162 / % possible obs: 100 % / Redundancy: 22.6 % / CC1/2: 0.999 / Net I/σ(I): 23.3
Reflection shellResolution: 1.58→1.61 Å / Num. unique obs: 23162 / CC1/2: 0.999

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GY6

5gy6


Resolution: 1.58→8.793 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 17.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1902 1129 4.91 %
Rwork0.1489 21864 -
obs0.1509 22993 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.08 Å2 / Biso mean: 21.3684 Å2 / Biso min: 7.37 Å2
Refinement stepCycle: final / Resolution: 1.58→8.793 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1499 0 32 207 1738
Biso mean--19.62 33.05 -
Num. residues----200
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A506X-RAY DIFFRACTION6.079TORSIONAL
12B506X-RAY DIFFRACTION6.079TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.58-1.65150.22851430.166226772820
1.6515-1.73790.20781350.158326932828
1.7379-1.84590.20061370.155127122849
1.8459-1.98690.22141370.153727042841
1.9869-2.1840.19371440.148927152859
2.184-2.49370.18341470.150627382885
2.4937-3.11840.19061450.152827512896
3.1184-8.79280.17251410.139528743015
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8366-0.53920.99343.1262-0.43571.7029-0.01610.0206-0.00580.05150.130.00550.05120.0312-0.10170.0606-0.00780.00530.0873-0.01460.085717.0035-8.1819-17.0519
22.3058-0.7488-0.15422.928-0.01072.9093-0.2419-0.2189-0.13760.47870.1535-0.0706-0.04730.10480.05080.22980.03810.0020.09520.00450.083234.7806-13.82872.851
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 100)A1 - 100
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 100)B1 - 100

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