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- PDB-7w05: 12 mutant Ribonuclease from Hericium erinaceus GMP binding form -

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Basic information

Entry
Database: PDB / ID: 7w05
Title12 mutant Ribonuclease from Hericium erinaceus GMP binding form
ComponentsRibonuclease T1
KeywordsDNA BINDING PROTEIN / catalytic activity enzyme anti tumor activity nucleic acid binding RNA binding
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 / Resolution: 1.29 Å
AuthorsTakebe, K. / Chida, T. / Suzuki, M. / Itagaki, T. / Morita, Y. / Uzawa, N. / Kobayashi, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20K21676 Japan
CitationJournal: To Be Published
Title: 12 mutant Ribonuclease from Hericium erinaceus GMP binding form
Authors: Takebe, K. / Chida, T. / Suzuki, M. / Uzawa, N. / Kobayashi, H.
History
DepositionNov 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 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

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Assembly

Deposited unit
A: Ribonuclease T1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0933
Polymers10,7031
Non-polymers3892
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint2 kcal/mol
Surface area5360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.589, 46.310, 53.524
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ribonuclease T1


Mass: 10703.474 Da / Num. of mol.: 1
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
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2 Å3/Da / Density % sol: 38.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Cadmium chloride hydrate, 0.1 M Sodium acetate trihydrate pH 4.6, 30% v/v Polyethylene glycol 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.19→46.31 Å / Num. obs: 22027 / % possible obs: 98.77 % / Redundancy: 2 % / CC1/2: 1 / Net I/σ(I): 33.78
Reflection shellResolution: 1.19→1.21 Å / Num. unique obs: 1444 / CC1/2: 0.821

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LS1

6ls1


Resolution: 1.29→11.9947 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1662 1089 4.95 %
Rwork0.1367 20910 -
obs0.1382 21999 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 62.79 Å2 / Biso mean: 15.4588 Å2 / Biso min: 6.1 Å2
Refinement stepCycle: final / Resolution: 1.29→11.9947 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms752 0 27 130 909
Biso mean--12.66 28.86 -
Num. residues----100
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.29-1.34870.22451340.17742349248392
1.3487-1.41970.17171270.157525912718100
1.4197-1.50850.16451340.13826362770100
1.5085-1.62470.16121420.133625912733100
1.6247-1.78770.15881300.13326412771100
1.7877-2.04530.14891340.125426402774100
2.0453-2.57260.17191400.128926682808100
2.5726-11.99470.16581480.139327942942100

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