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- PDB-1c0c: BOVINE PANCREATIC RIBONUCLEASE A DESICCATED FOR 4.0 DAYS -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1c0c
TitleBOVINE PANCREATIC RIBONUCLEASE A DESICCATED FOR 4.0 DAYS
ComponentsRIBONUCLEASE A
KeywordsHYDROLASE / HYDROLASE (PHOSPHORIC DIESTER / RNA) / DESICCATED / DRY / DEHYDRATED
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
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 (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsBell, J.A.
CitationJournal: Protein Sci. / Year: 1999
Title: X-ray crystal structures of a severely desiccated protein
Authors: Bell, J.A.
History
DepositionJul 15, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 1999Provider: 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 / Item: _software.name
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_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

Downloads & links

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Assembly

Deposited unit
A: RIBONUCLEASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3514
Polymers14,0631
Non-polymers2883
Water362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.700, 39.700, 50.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein RIBONUCLEASE A / E.C.3.1.27.5


Mass: 14062.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: PANCREAS / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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 / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 295 K / Method: small tubes / pH: 4.5
Details: 58% methanol (v/v), pH 4.5, SMALL TUBES, temperature 295K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Sep 14, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→99 Å / Num. obs: 4742 / % possible obs: 84.5 % / Observed criterion σ(I): 1 / Redundancy: 3 % / Biso Wilson estimate: 41 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 17.3
Reflection shellResolution: 2→2.2 Å / Rmerge(I) obs: 0.19 / % possible all: 64
Reflection
*PLUS
Lowest resolution: 9999 Å / Num. measured all: 14417

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Processing

Software
NameVersionClassification
bioteXdata collection
bioteXdata reduction
MERLOTphasing
TNT5Erefinement
bioteXdata scaling
RefinementResolution: 2→10 Å / Cross valid method: THROUGHOUT / σ(I): 1 / Stereochemistry target values: protgeo
Details: Final five cycles of refinement included all observed data
RfactorNum. reflection% reflectionSelection details
Rfree0.268 413 10 %random
Rwork0.185 ---
obs0.19 4363 84.3 %-
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms956 0 15 2 973
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg1.27
X-RAY DIFFRACTIONt_bond_d0.01
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / % reflection Rfree: 10 % / Rfactor obs: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg1.27
X-RAY DIFFRACTIONt_planar_d0.026
X-RAY DIFFRACTIONt_plane_restr0.008

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