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- PDB-1f0v: Crystal structure of an Rnase A dimer displaying a new type of 3D... -

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Basic information

Entry
Database: PDB / ID: 1f0v
TitleCrystal structure of an Rnase A dimer displaying a new type of 3D domain swapping
Components
  • 5'-D(*CP*G)-3'
  • RIBONUCLEASE A
Keywordshydrolase/DNA / domain swapping / crystal / ribonuclease / bovine pancreas / hydrolase-DNA COMPLEX
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 family signature. / Pancreatic ribonuclease / Pancreatic ribonuclease / Roll / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / DNA / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsLiu, Y.S. / Gotte, G. / Libonati, M. / Eisenberg, D.S.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: A domain-swapped RNase A dimer with implications for amyloid formation
Authors: Liu, Y.S. / Gotte, G. / Libonati, M. / Eisenberg, D.S.
History
DepositionMay 17, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 20, 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
M: 5'-D(*CP*G)-3'
N: 5'-D(*CP*G)-3'
O: 5'-D(*CP*G)-3'
P: 5'-D(*CP*G)-3'
A: RIBONUCLEASE A
B: RIBONUCLEASE A
C: RIBONUCLEASE A
D: RIBONUCLEASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,71736
Polymers57,1278
Non-polymers2,59028
Water9,980554
1
M: 5'-D(*CP*G)-3'
A: RIBONUCLEASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9299
Polymers14,2822
Non-polymers6487
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
N: 5'-D(*CP*G)-3'
B: RIBONUCLEASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,20612
Polymers14,2822
Non-polymers92410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
O: 5'-D(*CP*G)-3'
C: RIBONUCLEASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7457
Polymers14,2822
Non-polymers4635
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
P: 5'-D(*CP*G)-3'
D: RIBONUCLEASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8378
Polymers14,2822
Non-polymers5556
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.569, 96.341, 48.240
Angle α, β, γ (deg.)90.00, 107.50, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: DNA chain
5'-D(*CP*G)-3'


Mass: 573.430 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Protein
RIBONUCLEASE A / E.C.3.1.27.5 / RNASE 1 / RNASE A


Mass: 13708.326 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: PANCREAS / References: UniProt: P61823, EC: 3.1.27.5
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 554 / 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: 3.23 Å3/Da / Density % sol: 61.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Phosphate buffer, 16 % PEG 4000, 2 % Dioxane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1Phosphate buffer11
2PEG 400011
3Dioxane11
4Phosphate buffer12
5PEG 400012
6Dioxane12
Crystal grow
*PLUS
Details: drop contains protein and reservoir solution in a 1:1 ratio
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
22 mMdCpdG1drop
30.1 Mphosphate1drop
40.1 Mphosphate1reservoir
516 %PEG40001reservoir
62 %dioxane1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.072
DetectorDetector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 1.7→100 Å / Num. all: 76047 / Num. obs: 76047 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 14
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3 % / Rmerge(I) obs: 0.08 / Num. unique all: 7548 / % possible all: 95
Reflection
*PLUS
Lowest resolution: 40 Å / Num. measured all: 813673
Reflection shell
*PLUS
% possible obs: 95 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementResolution: 1.7→10 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.213 7651 11.2 %random
Rwork0.184 ---
all-75842 --
obs-68191 90 %-
Refinement stepCycle: LAST / Resolution: 1.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3804 152 164 554 4674
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg2.072
X-RAY DIFFRACTIONc_bond_d0.019
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Num. reflection all: 75824
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 25.14 Å2

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