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- PDB-1j80: Osmolyte Stabilization of RNase -

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Basic information

Entry
Database: PDB / ID: 1j80
TitleOsmolyte Stabilization of RNase
Components(RIBONUCLEASE PANCREATIC) x 2
KeywordsHYDROLASE / OSMOLYTE SOAKING / SARCOSINE / TRIMETHYLAMINE-N-OXIDE / BETAINE / TAURINE
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
Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsRatnaparkhi, G.S. / Varadarajan, R.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Osmolytes stabilize ribonuclease S by stabilizing its fragments S protein and S peptide to compact folding-competent states.
Authors: Ratnaparkhi, G.S. / Varadarajan, R.
History
DepositionMay 19, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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)13,4033
Polymers13,3072
Non-polymers961
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-23 kcal/mol
Surface area6430 Å2
MethodPISA
2
A: RIBONUCLEASE PANCREATIC
B: RIBONUCLEASE PANCREATIC
hetero molecules

A: RIBONUCLEASE PANCREATIC
B: RIBONUCLEASE PANCREATIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8066
Polymers26,6144
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area5400 Å2
ΔGint-51 kcal/mol
Surface area10900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.600, 44.600, 98.140
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein/peptide RIBONUCLEASE PANCREATIC / RNASE S


Mass: 1750.952 Da / Num. of mol.: 1 / Fragment: S PEPTIDE / Source method: obtained synthetically
Details: This peptide was chemically synthesized. It is naturally found in Bos Taurus
References: UniProt: P61823, EC: 3.1.27.5
#2: Protein RIBONUCLEASE PANCREATIC / RNASE S


Mass: 11555.981 Da / Num. of mol.: 1 / Fragment: S PROTEIN / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: pancreas / References: UniProt: P61823, EC: 3.1.27.5
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.75
Details: Ammonium Sulfate, cesium Chloride, pH 4.75, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
Method: unknown / Details: Kim, E.E., (1992) Biochemistry, 31, 12304.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112.5 mg/mlprotein1drop
26.0 M1dropCsCl
30.1 Msodium acetate1drop
480 %satammonium sulfate1reservoir
50.1 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 26, 1998
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→10 Å / Num. all: 5378 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.072
Reflection shellResolution: 2.1→2.3 Å / Redundancy: 3 % / Rmerge(I) obs: 0.098
Reflection
*PLUS
Lowest resolution: 10 Å

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Processing

Software
NameVersionClassification
XDSdata scaling
XDSdata reduction
X-PLORmodel building
X-PLOR3.851refinement
X-PLORphasing
RefinementResolution: 2.1→10 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.282 564 10.8 %RANDOM
Rwork0.218 ---
obs0.218 5300 75.5 %-
all-5378 --
Displacement parametersBiso mean: 20.6 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.26 Å
Luzzati d res low-3.8 Å
Luzzati sigma a0.3 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1140 0 5 123 1268
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_dihedral_angle_d28.3
X-RAY DIFFRACTIONx_improper_angle_d0.55
X-RAY DIFFRACTIONx_mcbond_it2.471.5
X-RAY DIFFRACTIONx_mcangle_it3.82
X-RAY DIFFRACTIONx_scbond_it6.092
X-RAY DIFFRACTIONx_scangle_it10.352.5
LS refinement shellResolution: 2.1→2.21 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.301 66 12.1 %
Rwork0.27 480 -
obs--56.9 %
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 1 / % reflection Rfree: 10.8 % / Rfactor obs: 0.204 / Rfactor Rfree: 0.27
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 20.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.55
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.301 / % reflection Rfree: 12.1 % / Rfactor Rwork: 0.27

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