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- PDB-3rid: X-ray structure of the C-terminal swapped dimer of P114A variant ... -

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Basic information

Entry
Database: PDB / ID: 3rid
TitleX-ray structure of the C-terminal swapped dimer of P114A variant of Ribonuclease A
ComponentsRibonuclease pancreatic
KeywordsHYDROLASE / ribonuclease fold
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
Chem-CGP / PHOSPHATE ION / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsMerlino, A. / Balsamo, A. / Mazzarella, L. / Sica, F.
CitationJournal: Biochimie / Year: 2012
Title: Chain termini cross-talk in the swapping process of bovine pancreatic ribonuclease.
Authors: Merlino, A. / Picone, D. / Ercole, C. / Balsamo, A. / Sica, F.
History
DepositionApr 13, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonuclease pancreatic
B: Ribonuclease pancreatic
C: Ribonuclease pancreatic
D: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,33512
Polymers54,7294
Non-polymers2,6068
Water9,836546
1
A: Ribonuclease pancreatic
B: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6676
Polymers27,3652
Non-polymers1,3034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-23 kcal/mol
Surface area13450 Å2
MethodPISA
2
C: Ribonuclease pancreatic
D: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6676
Polymers27,3652
Non-polymers1,3034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-23 kcal/mol
Surface area13480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.481, 96.948, 83.079
Angle α, β, γ (deg.)90.00, 106.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 13682.289 Da / Num. of mol.: 4 / Mutation: P114A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: RNASE1, RNS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical
ChemComp-CGP / 2'-DEOXYCYTIDINE-2'-DEOXYGUANOSINE-3',5'-MONOPHOSPHATE


Mass: 556.423 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H25N8O10P
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 546 / 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

CrystalDensity Matthews: 3.41 Å3/Da / Density % sol: 63.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 17-19% PEG 20000, 0.1M cacodylate, 100-150 mg/ml trehalose, 11mM dCpdG, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Nov 27, 2007 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.18→30 Å / Num. all: 38571 / Num. obs: 38571 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.074 / Net I/σ(I): 14.8
Reflection shellResolution: 2.18→2.26 Å / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 4.3 / % possible all: 99.4

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Processing

Software
NameClassification
DENZOdata reduction
AMoREphasing
CNSrefinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code 1F0V

1f0v


Resolution: 2.18→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.249 3047 RANDOM
Rwork0.181 --
all0.211 38551 -
obs0.188 30461 -
Refinement stepCycle: LAST / Resolution: 2.18→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3796 0 172 546 4514

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