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- PDB-9jwh: Crystal structure of native bovine pancreatic RNAs A -

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Basic information

Entry
Database: PDB / ID: 9jwh
TitleCrystal structure of native bovine pancreatic RNAs A
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
Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsAhmad, M.S. / Shah, N.
Funding support Pakistan, 1items
OrganizationGrant numberCountry
Not funded Pakistan
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)14,0427
Polymers13,7081
Non-polymers3346
Water2,072115
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.351, 64.351, 63.817
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-401-

HOH

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Components

#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
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.78 Å3/Da / Density % sol: 55.8 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 24-34% (NH4)2SO4, 0.1M sodium acetate buffer, super saturated NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 VENTURE / Wavelength: 1.5406 Å
DetectorType: BRUKER PHOTON 100 / Detector: CMOS / Date: Oct 13, 2022
RadiationMonochromator: Ni / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 1.85→17.84 Å / Num. obs: 13430 / % possible obs: 99.9 % / Redundancy: 3.8 % / CC1/2: 0.99 / Net I/σ(I): 20
Reflection shellResolution: 1.85→1.85 Å / Rmerge(I) obs: 0.769 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 827

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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: 1.85→17.84 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.11 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22301 671 5 %RANDOM
Rwork0.18236 ---
obs0.18441 12736 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.801 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: 1 / Resolution: 1.85→17.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms951 0 14 115 1080
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.013979
X-RAY DIFFRACTIONr_bond_other_d0.0020.018870
X-RAY DIFFRACTIONr_angle_refined_deg1.7791.6541326
X-RAY DIFFRACTIONr_angle_other_deg1.4881.5872015
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1045123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.45423.95848
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.81215168
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.289154
X-RAY DIFFRACTIONr_chiral_restr0.0880.2134
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021128
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_it2.1452.157495
X-RAY DIFFRACTIONr_mcbond_other2.1462.156494
X-RAY DIFFRACTIONr_mcangle_it3.3673.228617
X-RAY DIFFRACTIONr_mcangle_other3.3653.229618
X-RAY DIFFRACTIONr_scbond_it3.5852.556483
X-RAY DIFFRACTIONr_scbond_other3.2072.506475
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9673.609697
X-RAY DIFFRACTIONr_long_range_B_refined6.86126.7911130
X-RAY DIFFRACTIONr_long_range_B_other6.40326.3171099
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 59 -
Rwork0.276 902 -
obs--100 %

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