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- PDB-4g8v: Crystal structure of Ribonuclease A in complex with 5a -

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Basic information

Entry
Database: PDB / ID: 4g8v
TitleCrystal structure of Ribonuclease A in complex with 5a
ComponentsRibonuclease pancreaticPancreatic ribonuclease family
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-0EY / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.7 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

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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)27,7423
Polymers27,4172
Non-polymers3251
Water6,017334
1
A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0342
Polymers13,7081
Non-polymers3251
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)99.910, 32.569, 72.194
Angle α, β, γ (deg.)90.00, 90.53, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-315-

HOH

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Components

#1: Protein Ribonuclease pancreatic / Pancreatic ribonuclease family / 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-0EY / 1-{[1-(alpha-L-arabinofuranosyl)-1H-1,2,3-triazol-4-yl]methyl}-2,4-dioxo-1,2,3,4-tetrahydropyrimidine


Mass: 325.277 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H15N5O6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 334 / Source method: isolated from a natural source / Formula: H2O

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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: 2.14 Å3/Da / Density % sol: 42.58 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 25% PEG 4000, 20 mM Nacitrate, pH 5,5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
PH range: 5,5

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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 20, 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: 1.7→30 Å / Num. all: 25105 / Num. obs: 25105 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 12.87 Å2 / Rsym value: 0.051 / Net I/σ(I): 15.1
Reflection shellResolution: 1.7→1.79 Å / Mean I/σ(I) obs: 3.2 / Num. unique all: 1956 / Rsym value: 0.195 / % possible all: 78.1

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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: 1.7→13.487 Å / SU ML: 0.18 / σ(F): 1.37 / Phase error: 22.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2374 1269 5.05 %RANDOM
Rwork0.1875 ---
obs0.19 25105 96.77 %-
all-25105 --
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.065 Å2 / ksol: 0.42 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.0478 Å20 Å2-0.6805 Å2
2--0.732 Å20 Å2
3----0.7798 Å2
Refinement stepCycle: LAST / Resolution: 1.7→13.487 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1902 0 23 334 2259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071987
X-RAY DIFFRACTIONf_angle_d1.2712678
X-RAY DIFFRACTIONf_dihedral_angle_d14.005730
X-RAY DIFFRACTIONf_chiral_restr0.073298
X-RAY DIFFRACTIONf_plane_restr0.005350
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.7680.29481070.22931956X-RAY DIFFRACTION73
1.768-1.84830.23361330.19762652X-RAY DIFFRACTION97
1.8483-1.94550.2361270.19142750X-RAY DIFFRACTION100
1.9455-2.0670.24121440.19092701X-RAY DIFFRACTION100
2.067-2.22590.25581680.19382689X-RAY DIFFRACTION100
2.2259-2.44870.26591410.19642742X-RAY DIFFRACTION100
2.4487-2.80030.2681370.20092761X-RAY DIFFRACTION100
2.8003-3.51770.22411610.18052745X-RAY DIFFRACTION100
3.5177-13.48710.20431510.16862840X-RAY DIFFRACTION100

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