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- PDB-2xoi: Functional and Structural Analyses of N-Acylsulfonamide-Linked Di... -

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Basic information

Entry
Database: PDB / ID: 2xoi
TitleFunctional and Structural Analyses of N-Acylsulfonamide-Linked Dinucleoside Inhibitors of Ribonuclease A
ComponentsRIBONUCLEASE PANCREATICPancreatic ribonuclease family
KeywordsHYDROLASE
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-SFB / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBOS TAURUS (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsThiyagarajan, N. / Smith, B.D. / Raines, R.T. / Acharya, K.R.
CitationJournal: FEBS J. / Year: 2011
Title: Functional and Structural Analyses of N-Acylsulfonamide-Linked Dinucleoside Inhibitors of Ribonuclease A.
Authors: Thiyagarajan, N. / Smith, B.D. / Raines, R.T. / Ravi Acharya, K.
History
DepositionAug 17, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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

Downloads & links

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Assembly

Deposited unit
A: RIBONUCLEASE PANCREATIC
B: RIBONUCLEASE PANCREATIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5944
Polymers27,4172
Non-polymers1,1772
Water5,098283
1
A: RIBONUCLEASE PANCREATIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2972
Polymers13,7081
Non-polymers5891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RIBONUCLEASE PANCREATIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2972
Polymers13,7081
Non-polymers5891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.787, 33.146, 72.748
Angle α, β, γ (deg.)90.00, 90.94, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein RIBONUCLEASE PANCREATIC / Pancreatic ribonuclease family / RNASE 1 / RNASE A / BOVINE PANCREATIC RIBONUCLEASE A


Mass: 13708.326 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: SUPPLIER IS SIGMA / Source: (natural) BOS TAURUS (cattle) / Organ: PANCREAS / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical ChemComp-SFB / (2S,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-N-[[(2S,3S,4R,5R)-5-(2,4-DIOXOPYRIMIDIN-1-YL)-4-HYDROXY-2-(HYDROXYMETHYL)OXOLAN-3-YL]METHYLSULFONYL]-3,4-DIHYDROXY-OXOLANE-2-CARBOXAMIDE


Mass: 588.548 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28N8O11S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.17 Å3/Da / Density % sol: 44 % / Description: NONE
Crystal growpH: 5 / Details: 25 % PEG 4000, 20 MM NA CITRATE PH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.96
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 11, 2004 / Details: MIRRORS
RadiationMonochromator: SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 1.72→50 Å / Num. obs: 26200 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 18.12 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.23
Reflection shellResolution: 1.72→1.78 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 5.7 / % possible all: 92.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AFU

1afu


Resolution: 1.72→72.74 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.916 / SU B: 2.485 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24551 1310 5.1 %RANDOM
Rwork0.21541 ---
obs0.21693 24356 98.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.889 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20.17 Å2
2--0.13 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.72→72.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1877 0 49 283 2209
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0211970
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0061.9562673
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.355242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.43725.22788
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.87215327
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.834158
X-RAY DIFFRACTIONr_chiral_restr0.0620.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211480
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4511.51226
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.8521977
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.0343744
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.7324.5696
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.718→1.762 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 93 -
Rwork0.278 1736 -
obs--95.66 %

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