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- PDB-9jwd: Crystal structure of RNAs A treated with sodium cyanide -

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Basic information

Entry
Database: PDB / ID: 9jwd
TitleCrystal structure of RNAs A treated with sodium cyanide
ComponentsRibonuclease pancreatic
KeywordsHYDROLASE
Function / homology
Function and homology information


pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / defense response to Gram-positive bacterium / lyase activity / extracellular region
Similarity search - Function
Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease
Similarity search - Domain/homology
CYANIDE ION / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsAhmad, M.S. / Shah, N.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2024
Title: Cyanide mediated conformational changes resulted in the displacement of sulfate ion from the active site of bovine pancreatic ribonuclease A.
Authors: Shah, N. / Akbar, Z. / Ahmad, M.S.
History
DepositionOct 10, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0297
Polymers13,7081
Non-polymers3216
Water1,838102
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.329, 64.329, 64.102
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-390-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 13708.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P61823, EC: 3.1.27.5

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Non-polymers , 5 types, 108 molecules

#2: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CN / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.79 Å3/Da / Density % sol: 55.96 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M sodium acetate buffer pH 5.5. reservoir solution containing 24-34% (NH4)2SO4, 0.1M sodium acetate buffer pH 5.5, and super-saturated solution of NaCl.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.5406 Å
DetectorType: BRUKER PHOTON 100 / Detector: CMOS / Date: Mar 13, 2023
RadiationMonochromator: Ni / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 2.22→22.71 Å / Num. obs: 7822 / % possible obs: 99.3 % / Redundancy: 10.5 % / Biso Wilson estimate: 16 Å2 / CC1/2: 0.96 / Net I/σ(I): 1.44
Reflection shellResolution: 2.22→2.22 Å / Num. unique obs: 683 / Rpim(I) all: 0.521

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PROTEUM PLUSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EIC

1eic


Resolution: 2.22→22.71 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.838 / SU B: 7.121 / SU ML: 0.17 / Cross valid method: THROUGHOUT / ESU R: 0.26 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25752 342 4.4 %RANDOM
Rwork0.20091 ---
obs0.2034 7462 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.002 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.22→22.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms951 0 16 102 1069
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.013981
X-RAY DIFFRACTIONr_bond_other_d0.0010.018876
X-RAY DIFFRACTIONr_angle_refined_deg1.5171.6541325
X-RAY DIFFRACTIONr_angle_other_deg1.3171.5872029
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7995123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.53123.95848
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.70615168
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.857154
X-RAY DIFFRACTIONr_chiral_restr0.0660.2134
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021128
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02220
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_it1.2521.499496
X-RAY DIFFRACTIONr_mcbond_other1.2541.498494
X-RAY DIFFRACTIONr_mcangle_it2.1972.244617
X-RAY DIFFRACTIONr_mcangle_other2.1952.244618
X-RAY DIFFRACTIONr_scbond_it1.3281.655484
X-RAY DIFFRACTIONr_scbond_other1.2951.634481
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2452.381703
X-RAY DIFFRACTIONr_long_range_B_refined4.74118.4591124
X-RAY DIFFRACTIONr_long_range_B_other4.43618.4311115
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.224→2.281 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 17 -
Rwork0.294 504 -
obs--93.2 %

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