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- PDB-4g8y: Crystal structure of Ribonuclease A in complex with 5b -

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Basic information

Entry
Database: PDB / ID: 4g8y
TitleCrystal structure of Ribonuclease A in complex with 5b
ComponentsRibonuclease pancreatic
KeywordsHydrolase/Hydrolase Inhibitor / nuclease / Hydrolase-Hydrolase Inhibitor complex
Function / homology
Function and homology information


pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / lyase activity / defense response to Gram-positive bacterium / extracellular region
Similarity search - Function
P-30 Protein / Ribonuclease A-like domain / Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-0FT / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsChatzileontiadou, D.S.M. / Kantsadi, A.L. / Leonidas, D.D.
CitationJournal: Bioorg.Med.Chem. / Year: 2012
Title: Triazole pyrimidine nucleosides as inhibitors of Ribonuclease A. Synthesis, biochemical, and structural evaluation.
Authors: Parmenopoulou, V. / Chatzileontiadou, D.S. / Manta, S. / Bougiatioti, S. / Maragozidis, P. / Gkaragkouni, D.N. / Kaffesaki, E. / Kantsadi, A.L. / Skamnaki, V.T. / Zographos, S.E. / ...Authors: Parmenopoulou, V. / Chatzileontiadou, D.S. / Manta, S. / Bougiatioti, S. / Maragozidis, P. / Gkaragkouni, D.N. / Kaffesaki, E. / Kantsadi, A.L. / Skamnaki, V.T. / Zographos, S.E. / Zounpoulakis, P. / Balatsos, N.A. / Komiotis, D. / Leonidas, D.D.
History
DepositionJul 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)27,7563
Polymers27,4172
Non-polymers3391
Water4,432246
1
A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0482
Polymers13,7081
Non-polymers3391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ribonuclease pancreatic


Theoretical massNumber of molelcules
Total (without water)13,7081
Polymers13,7081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.301, 32.672, 72.380
Angle α, β, γ (deg.)90.00, 89.35, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ribonuclease pancreatic / RNase 1 / RNase A


Mass: 13708.326 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: pancreas / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical ChemComp-0FT / 1-{[1-(alpha-L-arabinofuranosyl)-1H-1,2,3-triazol-4-yl]methyl}-5-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidine


Mass: 339.304 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H17N5O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O
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: 2.16 Å3/Da / Density % sol: 43.13 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 25% PEG 4000, 20 mM Nacitrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.54178 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Nov 21, 2011
RadiationMonochromator: Cu-K / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 22087 / Num. obs: 22087 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.12 % / Biso Wilson estimate: 13.65 Å2 / Rsym value: 0.1 / Net I/σ(I): 12.4
Reflection shellResolution: 1.8→1.9 Å / Mean I/σ(I) obs: 2.8 / Num. unique all: 2588 / Rsym value: 0.441 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.3_928)refinement
REFMACrefinement
CrysalisProdata collection
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2G8Q

2g8q


Resolution: 1.8→13.884 Å / SU ML: 0.22 / σ(F): 1.37 / Phase error: 23.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1126 5.1 %Random
Rwork0.1988 ---
obs0.2018 22086 99.93 %-
all-22086 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.59 Å2 / ksol: 0.413 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→13.884 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1902 0 24 246 2172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061977
X-RAY DIFFRACTIONf_angle_d1.1652664
X-RAY DIFFRACTIONf_dihedral_angle_d13.401724
X-RAY DIFFRACTIONf_chiral_restr0.073295
X-RAY DIFFRACTIONf_plane_restr0.006348
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.88180.33211210.24092588X-RAY DIFFRACTION100
1.8818-1.98080.26411450.20282566X-RAY DIFFRACTION100
1.9808-2.10450.22961520.19252604X-RAY DIFFRACTION100
2.1045-2.26630.22021200.19232622X-RAY DIFFRACTION100
2.2663-2.49320.26161420.20122633X-RAY DIFFRACTION100
2.4932-2.85130.28291450.21652594X-RAY DIFFRACTION100
2.8513-3.58210.26191430.20062654X-RAY DIFFRACTION100
3.5821-13.88470.24611580.18012699X-RAY DIFFRACTION100

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